I hand draw my comics on paper and ink them with Microns, then scan it into Photoshop.
My biggest pet peeve with my process is in Photoshop, where one single empty pixel on each line is what WILL cause the paint bucket to fill EVERYTHING. I then have to undo and hunt down the wayward pixel.
At this point, I feel like Photoshop would have a setting where one could designate a "pixel gap," that would permit Photoshop to understand that I am trying to fill in one space, not the whole panel.