How can I raise rep with them so I can get access to their adv workbench? Atm I'm at -12 and I need 900 positive rep.
Work for them.
Specifically, there's a few things you can do.
1. Do the "Retrieve the Manufacturing Plans" from the Mutant cave thing, which you'll need a somewhat strong character or a few people for. It's an automatic 500 rep, I think. You'll need a lockpicker as well.
2. Easier, is to deliver briefcases to various places for the rep. You'll have to do a few of them, and I think there's a timer on it so you can't do them all in a row. You'll have to check.
In both instances, talk to Marshall (the guy who gives the 10% bonus thing) about working for them.