There are some easy ways to prevent this.
Example 1: Colouring with low brush transparency.Same situation as you've got:
![](http://img227.imageshack.us/img227/8813/1324234234jg8.th.jpg)
Leave brush colour and set transparency to 25-35%; make few clicks:
![](http://img227.imageshack.us/img227/5294/2tn6.th.jpg)
You'll get something like this:
![](http://img226.imageshack.us/img226/2162/3uk0.th.jpg)
Now it's very difficult to find the border between colours:
Example 2: Using of Average Vertex Colours function.
Single-coloured polygons:
![](http://img226.imageshack.us/img226/2492/5jj0.th.jpg)
Some shading:
![](http://img204.imageshack.us/img204/2746/6nx8.th.jpg)
Select wanted vertex:
![](http://img205.imageshack.us/img205/2719/7ts6.th.jpg)
Press Ctrl+G or PolyWorks Main menu=>Edit=>Average Vertex Colours. You'll got something like this:
![](http://img204.imageshack.us/img204/5263/8ke1.th.jpg)
Now it's very difficult to find the border between colours:
![](http://img204.imageshack.us/img204/9196/9nr6.th.jpg)