Well you could always manually setup the second install in a different folder, such as yourdomain.com/testing/ and then one install of Joomla wouldn't even know there was another one there.

That's what I've done, but don't forget to either use a second database for your second installation, or at the very least, use a different db prefix. Ie: jos_ for one site, and jtest_ for your test site, as an example. But, if you use a seperate db then by all means, use jos_ for both
