SQL Source Control doesn't currently have great support for branching - it's something we've heard a lot of customers asking for, and we're focusing on it right now.
Given that, I'm afraid there's not really much I can recommend - if you're relying heavily on branching, there's no guarantee that SQL Source Control is going to be able to cope with that well. By all means try, and if you do run into any issues let us know and we'll do our best to get them ironed out, but for the time being this is largely uncharted waters for us. Sorry!
Andy Campbell Smith
Red Gate Technical Support Engineer