You would need to open the formulas in something that can open EPS files, like Illustrator - and add the colour there.
You can use Color directly in MathType in equations saved in eps format. If the thing is more complicated you can follow Eugene proposal and do the job in Illustrator.
Perhaps it's better if you include a typical example of what you want to do...
Thanks for your answers. The thing is when you make color changes in Mathtype you can't change them into CMYK, which is a big disaster, when you have a scientific report (180p) that needs to be printet. It also slows down the entire workflow.
Somehow I think Indesign needs to improve this problem in their next version:)
Of course MathType supports CMYK:
Is the problem that when you change to CMYK, the preference doesn't stick? Or did we not make the CMYK choice easy enough to find? (That question isn't intended as an insult; I honestly want to know. If a feature is too hard to find, we should either make it easier to find directly in the UI or improve the documentation to describe it better.)