A little late, but you might still have a use for this info, so here goes:

If you have VS 2003 (or later :), you can use the "Only build startup
projects and dependencies on Run" option in Tools/Options
(Environment/Projects and Solutions). If you turn it on, build manager will
only build the startup project (and the ones it depends on) in your solution
and ignore the rest, so just set your experimental project as the startup
one and you're all set.
If you have VS 2002, that option is not there, but you can simply unload the
main project (available from the Project menu) while you run your other
project. Then reload it back. It's a bit uglier, but works.

hope that helps,
Lukasz