Well, there are some ways to install several instances of nagios on one account with only one nagios installation...
BUT, it's really hard to implement, and, in the end, quite useless
IMHO, the best (and simplest) way to accomplish this is what we did:
create a new account for each instance (nagios, nagios2, nagios3 ...etc), make separate installations (as if the others don't exist) and enjoy
Hope this helps