Today, each project does indeed have just one dictionary file. One thing you could do is create a project that has a dictionary of common terms and then use that dictionary as the starting point for new projects. Here are some details on how you would do that: http://casecomplete.zendesk.com/entries/256462-changing-your-project-dictionary
The good news is, what you're asking for has been a much requested feature, so we're working on it right now. We'll have a much better solution for managing dictionaries in the next release.