You can run as many projects simultaneously as you like!

Simply add the project from the BOINC interface, or the command line if you prefer, or even from BAM. Your machine will then evenly divide its compute power across the projects, unless you manually change the split.

If you want to stop running a specific project for a while, just set it to receive no new work units. This way it is easy to resume work on it later, and you will finish any work already sent out to your machine by the project server, which is good manner. =)