If you want to use multiple colors on a single .STL file then your only option are:
- Use a Z-pause to swap materials;
- Use different processes (S3D) with different starting heights that both use different nozzles.

But, these effect both only can change the color per LAYER.

If you want to change the color of a piece of the .STL independent of layer (aka, multiple colors on a single layer) then you need to split the .STL file.
For this you can use any CAD/modeling software that you like and/or Google ways to split the model, because you will need 2 .STL files (that combine together as one) to use 2 different nozzles.