.prj files are intended to be shared by different developers, so I would think you should be able to have a single .prj file that can be copied back and forth between your two computers. The only impediment to sharing a .prj file would be if you cannot build a relative path from one location to another (for instance, if some paths in one computer are in a different drive from the other computer).
.cws files, on the other hand, might be harder to share, and since this is where your tags are persisted, this would still be a problem. Hasving said that, I know of cases where people have successfully been able to share .cws files.
If I were you, I would first try to share the .prj and the .cws files across both computers, to see what problems you might run into. There's a chance that they might be solvable.
Luis