Yojimbo does not support multiple databases. If you want a per-project
database, you may want to take a look at Eagle Filer which does not
store data in a monolithic database and allows you to use separate
libraries for each project. I use Yj for miscellaneous data such as
passwords, etc. and Eagle Filer for project-specific data. Not as
elegant as a single app but I find this works better than sticking
everything in Yj.
http://c-command.com/eaglefiler/
Cheers,
Rhet