There are some easy ways to prevent this.
Example 1: Colouring with low brush transparency.Same situation as you've got:
Leave brush colour and set transparency to 25-35%; make few clicks:
You'll get something like this:
Now it's very difficult to find the border between colours:
Example 2: Using of Average Vertex Colours function.
Single-coloured polygons:
Some shading:
Select wanted vertex:
Press Ctrl+G or PolyWorks Main menu=>Edit=>Average Vertex Colours. You'll got something like this:
Now it's very difficult to find the border between colours: