Two trims tanks in this case... well I don't think the rear bag will affect the linkages as long as you keep it in a compartment of some sort, wouldn't want something "growing" bigger and bigger inside your sub!

I think that the idea of bladder bags is also known as the RCABS ballast system, I've heard that they work really well, check out the SubCommittee message boards, I've come across a lot of folks who are satisfied with the results. Can you give me the site that you ordered your sub from?