I'm working on my first substantial programming project, a big statistical analysis in Matlab of a few overlapping data sets and lots of collinearity issues. Since I have no programming experience, it's becoming a big mess... lots of scripts interacting with the data, me trying to write scripts to address problems as they pop up, and too many variables in my workspace. Could someone help me out by sharing best practices on how to manage programming projects?

I'm going to be working on this for a while, so if you have book suggestions or MIT/Stanford classes that address this type of issue I'd love to hear about them.

Thanks!