Off the bat, each set of bands should work at each respective hotel.
Beyond that- both sets SHOULD work (or one set at both places), if they are linked properly in the new system.
The short answer is that you should bring your bands to the front desk when you check-in. They can make sure the set you want to sue is properly activated.
We also have multiple sets of bands now.
There is a slight chance that a set won't work in a given location (parks, room, dining, pool access - if applicable) but they are supposed to all be linked.
My always advice, bring ID and back up ($, cc) whenever you leave your resort.
We had glitches with our bands in Jan, and it took a couple trips to the front desk to get it all fixed. I'm thinking they have improved the system since then, but in my opinion, it's far easier to carry a cc my pocket then it is to be told I can't use a FP or buy food until I get over to Guest Services.