You can specify an rc file for csh to invoke after the usual ones (that is, /etc/csh. and $HOME/{.cshrc,.login}) with the -m flag. You could keep all the shared configuration in .cshrc and move the project-specific things to their own rc files, and just start a new csh session from within your existing one whenever you want to work on your project like so:
exec csh -m .cshrc.project1 This has the added advantage that project-specific variables don't get in the way during your regular shell use. The downside is that you'll need to do this in every new terminal window. How much of a pain that is depends on your workflow.