Yes. You just need to make sure that you run each instance with a different userdir .
If you try to run a second NetBeans instance with the same userdir you will get a warning that another instance might be running and you should consider stopping the new one. Ignoring this warning and running two instances on top of the same userdir definitely isn't a good idea.
Applies to: NetBeans 3.6, 4.0, 4.1, 5.0
Platforms: All