You didn’t say which program you are using, so I took screenshots of how I got two different colored eyes in Carrara 8.5, Poser 7, and DS 4.5 using Shader Mixer. I used Genesis in Carrara and DS, and V4 in Poser, all with the default V4 textures.
The eyes in Genesis and Mill4 figures are mapped so you can use an image that’s black on one side and white on the other to control a node to mix the two textures. Feel free to use the image I’m posting.
Carrara - Mixer
DS - Mix
Poser - Blender
In Poser and DS you need to use a Blender/Mix node for each channel with textures you want to mix (1 for diffuse, 1 for bump, etc.).
In Carrara you can put a mixer in each channel, but it’s easier to use a MultiChannel Mixer.