I’m doing Flat Painting, and wanted to “erase” some of my work, does that mean I have to paint with the canvas color?
If I use the Eraser Tool then it also goes through the canvas. Since you have to “prime” the background before you do flat painting.
Whats the best way to erase when flat painting? 
Use ‘Undo’… (CTRL-Z)
You can set the number of ‘undos’ in ‘Preferences’…
Don’t forget to use different layers…It can help. 
Characters on one layer and the scenery on other one.
Hello,
I tend to have a set procedure to my flat paintings. For example, before I paint in the highlights I would duplicate the layer, use the highlight/colourise tool to achieve the effect, then erase back to the first layer. When your happy with the results, you can either keep the layers intact or collapse them using the merge option.
Be careful when collapsing layers. Make sure you have MRGB, ZAdd on, RGB & Z intensity to be 100 (I usually select the simple brush with these presets).
I currently have a couple of issues with regards to Merging down layers and have an open thread:
http://www.pixolator.com/zbc-bin/ultimatebb.cgi?ubb=get_topic&f=4&t=001867
Hope this helps.