A little advice regarding print-ready comics?

Here's a new Chicks Dig Cartoonists strip, the first one since my computer crashed. I don't usually post these on my blog since it has its own site, but I posted this one to ask for some help.

You see, none of my comics are print-ready, so if I wanted to make a mini comic or something and printed these, they'd all be pixely or blurry. To make them at a higher DPI though, I'd half to redo half the comic.
My current process is this: I draw the comic in Flash, leave in what's solid black and white, and the rest transparent, and then export it as a PNG. After that, I open up the PNG in Photoshop to do the screentones. Because I like screentones. That makes most of the problem, though. If I export the file from Flash at say 300 to 600 DPI (for print), the screentones are going to look different than if I export at something like 72 DPI (optimized for web). Basically the way I'm doing it, I'd have to do the screentones for each comic twice. Once at a 72 DPI, and once at a print-ready DPI.
Is there something I'm totally missing here? Is there a way I can do the comic and just have it look the same in print and on the web? I've thought about just doing the comics entirely in Photoshop, but I'm not as used to it as I am with Flash, so it'll take some practice. I dunno, maybe I'll figure something out, but any advice would be greatly appreciated.