I recently discovered this quicker way to color in flats in Manga Studio.   You can find the original post on my instagram page

1. make sure line art is a closed loop
2. use auto select tool
3. IMPORTANT go to tool property tab, make sure you turn on Area Scaling, dial it to 2 or 3.  This ensures alongside anti-aliasing that you wont have jagged pixely shaped flats (using the ‘expand selection’ tool also works)
4. create a new layer under lineart layer
5. choose your foreground colour, and hit alt + backspace to fill.
6. deselect by hitting ctrl+d

If you have any other tips i’d love to hear them!  Tweet them at me @drumok