Once the background is complete, there's a few more things you need to do. In this guide we'll talk in detail about how to put the sprites in your sprite comic as well as what to keep in mind when laying everything out.

Step 1: Who, what, where?

Before you start dropping sprites all over the place it's time to do some more planning. If you finished the backgrounds already then you should at least know where each panel is taking place. Now, you also need to know what characters, creatures, and/or items are going to be in each panel and what pose those things will be in so you know which sprites to copy over from your sprite sheets. Also, you should probably do some thinking about where those sprites are going to go in each panel. If you're using a program like Photoshop, this really isn't an issue since you can easily go to whatever layer you want and move it around until it's exactly where you want. In a program like Paint, however, once you place a sprite moving it is usually a real pain and often involves rebuilding parts of the background or other sprites that got damaged in the process.

Step 2: From the Sprite Sheet to the Comic Strip

Before you start moving sprites over, it's often helpful to have a bit of extra blank space beneath your strip (especially if you're using Paint). For example, a Pebble Version strip is 800 pixels wide and 200 pixels high. However, before I save the final version of any given strip, it's actually 600 pixels high, creating a large empty area beneath the strip itself. You can use this white space to store sprites and text before placing them on the actual strip. It helps keep things a lot less cluttered and makes some things a lot easier in Paint.

Now this is gonna change a bit depending on which image program you're using to make your comic. It's safe to say that in any program you could simply open your sprite sheet, draw a selection box around a sprite that you want, go to the Edit menu and hit Copy, then open your strip and go to the Edit menu and click paste to paste it in your strip. (Or you could just use Ctrl + C to copy and Ctrl + V to paste in nearly any Windows program.) After pasting the sprite in, it will remain selected and you can move it around to wherever you want before unselecting it and moving on. However, there are easier ways to do it in some programs while others may require a little more work. There's too many programs out there for me to cover each one so for now I'll just focus on the two that are most commonly used for sprite comics, MS Paint and Adobe Photoshop.
Note: As a rule, it'll make things a lot easier if the background color of your sprite sheets is not used in any of the sprites on that sheet. Transparent backgrounds are ideal and very easy to do in nicer programs like Photoshop. Although there are also many programs where you won't have that ability.

In Photoshop: Now this is easy. You can have multiple documents open at a time so open both your comic strip and your sprite sheet. Look at the sprite sheet and find the sprite you want. If it's on its own separate layer just use the move tool to drag it off of the entire sheet and then drop it right onto your comic. If the sprite isn't on its own layer then just drawn a rectangular marquee (or whatever type of marquee you like) around it, switch to the move tool, drag it off the sprite sheet entirely and drop it onto the strip. Either way, the sprite will end up in you comic strip file on a new layer of its own. All you have to do now it rename the layer to something descriptive so you can always find it later (for example "Brendan Panel 1" or "Falling Sonic") then move it up or down in the layer stack and finally move it around and place it exactly where you want it in the strip.
Note: These instructions are for sprite sheets that have a transparent background. If you have a solid color background instead, you can remove it with the Magic Eraser tool (make sure the tolerance is set to 0 and the Anti-Aliasing box is unchecked then select the layer with the background color, click said color to select it, and hit delete. Note: If the background color isn't used in the sprites themselves go ahead and unchecked the Contiguous box when you do this. If it is used in the sprites you're better off having the box checked and manually removing any stray bits of background that remain in the gaps or holes in the sprites (for example, a gap between the sprite's arm and body).

In Paint: This is a little trickier. First off, Paint doesn't let you open multiple files at once so you'll have to do the next best thing and open Paint multiple times.  First start Paint and open your comic strip. Then open Paint again (so you have two copies of Paint running) and open your sprite sheet. Note: The order is actually important. Depending on your version of Windows and Paint, things might not paste correctly (or even at all) if you open them in the opposite order.
With that taken care of find the sprite you want on your sprite sheet and draw a rectangle around it with the select tool. Go to the Edit menu and copy your selection. Now go to the Paint that has your strip in it, go to Edit again and hit paste. You sprite will appear and it will be selected. Make sure not to change tools or click outside the selected area. First drag the sprite down to your white space below the strip. Now, if the background color from your sprite sheet isn't white use the paint bucket tool (aka the fill with color tool) to change it to white (change your foreground color to white, click on the paint bucket tool, then click on the background color surrounding your sprite).
When you're ready to put the sprite in its proper place on top of your background use the select tool and draw a box around the the sprite. Now, here's the important part. There will be two large buttons beneath the main tool bar on the left. If you click on the top one, then you'll not only be moving the sprite but all that white background that's also selected. You don't want that so click on the second button then go down to the color bar at the bottom and right click on the white. This will set your background color to white. Now you can drag your sprite into place without having to worry about the background color.
Basically, what you're doing is telling the selection tool to ignore anything in the current selection that's the same color as the background color, which you choose by right clicking on a color in the color bar. This will probably cause problems if that color happens to be a part of the sprite. So if your sprite, for example, happens to have some pure white in it you might want to use the paint bucket and change your white space to some other color that isn't used in the sprite.
And that's that. Just keep in mind that moving the sprite after its already been placed over your background is usually a real pain so make sure it's exactly where you want it before deselecting it.

Step 3: What to Leave Room For

While you're placing your sprites, make sure you remember to leave enough space for any other sprites you want to add in. Also, if there's going to be text and/or speech bubbles you'll need to leave plenty of room for those as well. If you're working in Photoshop you can play around with the placement of your text and sprites until they're perfect. In Paint you'll just have to be careful and leave plenty of extra room (most likely at the top or bottom of your strip) to fit your text in later.

Step 4: Finishing Touches

We'll be going over things like text, speech bubbles, and special effects in later parts of the guide but you should still keep in mind what you want and where you want it to go. Also, if you're using a program like Paint that doesn't have layers and you may want to put some things on top of your characters (for example to make it look like they're walking in the grass instead of on top of it or behind a tree instead of in front of it).

Conclusion:

Once you know how to do it, adding sprites to your comics really isn't very hard. Programs that use layers, like Photoshop, make it a lot easier to move and tweak your sprites later on but you can still do more or less whatever you want in the simpler programs as well as long as you're careful and plan things out a bit more in advance. Try creating a strip, putting in the background, and arranging the sprites in your image editor. Practice until you feel comfortable with everything then take a look at Josiah's Sprite Comic Guide Part 5: Script Writing 101.