If you really wan to micro manage, the only way to make BOINC work exactly as you want is to run one project at a time. Let's say you want SETI 80% and Einstein 20%. Then run run SETI for 4 weeks, an then Einstein for 1 week.

Even using app_config.xml cannot get the job done, with the convoluted BOINC code. Eventually one project will over load, go into panic mode, and leave you with idle threads.