Soo.. you wan't to use a Bentley product with Intergraph... Hmm... Poke
Just kiddin.

It shouldn't be a problem.
What you have to work with is causing the correct cfg to be loaded per project. Projectwise can easily be scripted to copy the appropriate project cfg and (perhaps) overwrite the local version before opening the file. -- Unless you don't use databases and you only use one set of specs and libs, etc.

Another feature that might need to be turned on (or disabled, depending on how you look at it), is: The cfg has an entry for SaveLastProfileUsed=0. Would probably need to be changed to 1 unless you select a profile through ProjectWise.