Digital here too... first I was using Photoshop but then I picked up Manga Studio/Clip Studio Paint and do most everything in it.
Setup I work to scale. My size is 6.88 x 10.5 with a live area of 6x9, I think it looks nice and centered on the page. Resolution is high of course! 600 dpi is more than enough as most printers I've encountered want 300 dpi. So scaling down is pretty simple.
After the script I draw out the entire comic in rough layouts (in CSP), as I do the lettering-- I find that it helps me to figure out the panels if I know where the text is going. I use a 21UX Cintiq. Lettering is done with CSP. At first it was totally confusing, but I can't see myself going back to Illustrator. There are some things I haven't figured out yet, but I think the tools are there-- just need more time to play with it.
After rough layouts I use the Rectangle Frame tool to fill up my 6x9 area (it snaps) and then use the Divide Frame Folder tool to make my panels. I pencil either inside or outside the frame folders (depends on the page). I keep my Copy as the top/highest layer for easy editing. If I need the tail to reach the end of the frame, I copy and past that speech bubble into the frame folder so the tail is within the frame mask.
Ink and Coloring are all in the frame folders for the most part. I typically ink with the G Pen between 8-15 size. Exporting is easy, I set the scale down to either 25 or 20% and batch export. I try to finish a few pages at a time before I export... I typically export PNGS.
When I'm finished with the issue, I save a duplicate and merge everything down. I always try to have two copies.