Lesson 2: Backgrounds and Borders

Comics are kind of bland if you put the sprites up against an empty white background, and troublesome to make if you don't establish a standard framing format. The format is the number of panels you'll have, how they're arranged, and how big they are. It's best to start with nice, square panels which you can easily make with the line tool in Paint. Size your panels based on how big you'll be making the sprites and how many of them you expect to stuff into a scene at maximum. Take into account that you'll be adding backgrounds.
The Nintendo Acres sets are about 99% hand-made, which accounts for the flat look. It's hard to make textures and patterns in Paint unless youv'e got the time, patience, a knack for working with the Colors screen, and the willingness to build a few pixels at a time. I lack all of these. Anything in NA that is textured, patterned, or looks like something besides flat rectangles of color with the occasional curve to it, I took from background sprite sheets. TSR had some good backgrounds and background kits, as does MFZ if you're in the market for Sonic sets. I hear that, with the right expansions and add-on files, RPG Maker 2000 or higher is a good program for building sets.
Whether ripping or building, if your comic doesn't revolve around a long journey, or an actual video game, then you should set your backgrounds at maximum zoom-out and trimmed to fit your largest standard frame and put all of them in one file, saved as Sets, Backgrounds, or whatever. If you still wind up using a lot of sets, but using them frequently, you'll have a big file after awhile. So you may consider saving the backgrounds in multiple, categorized files for easy referencing.