Robert,
I have a very similar situation for the above posted. I think you guys need to think about different kinds of setups people have. Your software looks amazing, I've been cruising around examining different web ranking software, and this is a very good one.
However, it's functionality is somewhat limited by it's scope of having 1 set of keywords per project. What I mean is this...
Much like the above user, I have about 250 sites, with about 500 keywords I want to check them for. I DO NOT want to check all 250 sites for all 500 keywords, but rather each site has a very specific 1-2 keywords to monitor.
If I were to setup 250 projects, it would seem as if there is no easy way for me to see all 250 at once.
However, if I could put all of these sites into the same project, and then add in the keywords for each specific domain, it would be perfect!!! I could see everything more or less at once.
As it stands, your very nice software appears useless in my situation. And I can promise you that there are many other people looking for a solution to their very similar situations.