Can we separate categories and/or brand?

Yes, you decide what categories or brands to include in the feed BidBrain use.

Yes you can. You decide what categorires/brands you want to run with Bidbrain, and you do this through your product feed. If you only want to run 1 or 2 product categories with Bidbrain you simply just send these categories to Bidbrain via your feed. The same rule applies here as in the question regarding running separate Google Shopping campaings with Bidbrain. As long as you are not running the same products or product categories in your own Google Shopping campaigns, then this is fine.