It's likely that Libraries are not the organization construct that you want. Separate libraries are a hard boundary for MC and should very rarely be used.
Generally speaking, when you want to have a top level organizational structure in MC, you should probably be using a view that specifies something: A top level directory for example. I know someone who separates his high resolution files from the regular ones. He has a top level view, in the left navigation pane, that says "hi res". Under that are multiple views like "album", "artist", etc. These only see his high resolution files because the top level HiRes view has a rule to only look in his HiRes folder.
You would need to duplicate these views into the JRemote views area also; JRemote uses separate views from desktop MC. But none of this is hard. It's just a little bit of work. If you have a lot of work into your existing libraries (views, etc) then this might be harder.
The key point here is that Libraries are a poor way of organizing music. They are more for hard boundaries between collections that would never be used together.
Best of luck.
Brian.