Desktop

I work for a startup software and we provide a e-learning platform in which to author, develop, distribute and manage content. We have a lot of customers who want just a few customizations. However as we grow we find it harder and harder to managethis. We come out with a new release about every 90 days plus point release on top of that for a bug fix here and there. Each we upgrade we are at a risk of loosing the customization or having it not work correctly. Dose anyone have a good proven methodolgy on how to do this?