I use Manga Studio for all of my comics. The initial concept was drawn on the back of an envelope. Then I did a refined sketch in Photoshop CS3 using a Wacom Tablet. I feel comfortable with PS and can work quickly on several layers without getting bogged down in details. I could have done it in Manga Studio but I was in the mood to do it that way. Finally I did the finished colour illustration (above) in Manga Studio. Several months passed between those stages as I had other priorities.
Here is the original sketch on the back of an envelope:
The refined sketch:
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