Drawing the stick figures is the easy part. If you don't know how, stick figures should be sort of balanced out, with their heads proportionate to their body. Try not to dress your figures up too much, it'll look weird.

Once you scan a comic in, the result will probably be very faint with faint blue lines if you used lined or graph paper. In Paint.NET, go to the Adjustments menu and select Brightness/Contrast. Set the brightness to -60 (yes, the white will be grey, we'll fix that next) and the contrast to 60. The two values being opposites causes the black to be darkened, but the white stays white.

You can then add in your words in whatever font you like (I use Futura Md with bold on) if your writing is messy (read: unreadable) or you like your comics to have nice clean TrueType writing! :P