This is honestly the only real question I get asked consistently. Yes, the term FAQ might not be entirely accurate. It's not a terribly complicated process, so here's a fun blog post about how I do this. There are actually two different methods I've used - whether I draw the comics by hand and just touch them up digitally, or whether I draw them almost entirely digitally. Since the second one will probably be not only easier to show you but a more interesting read, I'll focus on that one, since it's what I primarily use now, since I'm lazy. (which will be a running theme throughout this series of blog posts, trust me.)
First off, I write the comic. As of this blog post, I've completely written about half the Ratboy story. I constantly revise it and add little jokes as I see fit, change gags that seemed rushed or convoluted, and do my very best to not resolve things with Deus Ex Machinas - even though it's an occasionally funny and super convenient literary device. I have the rest of the story loosely lined out and write in whenever I feel like - which is why I write so far ahead because I get distracted easily.
When it comes time to actually draw the comic, I first draw a very rough outline for composition. This usually takes about sixteen seconds. I time myself. Mainly it takes such a short amount of time because I get lazy. I don't always have as much time as I'd like to draw these comics, and I wish I did, because I could get better compositions rather than lame ones. It really depends on if I'm in a hurry or not.
I tend to leave the backgrounds blank at this spot unless it's necessary, easier, or otherwise prudent, such as in the final panel pictured here. I do this mostly to give me more flexibility when reevaluating things like the composition for each page, and to make sure the backgrounds actually work with the much-more-important foreground.
Coming up in part two: Pencilling Like An Idiot