Hello, 
I have a few FPGA VI's that contains AI, AO, or DO (the way I wanted to group them).  Now, I have put these FPGA VI's as sub VI's in a top-level FPGA VI, and have linked them up like you normally would in other non FPGA Labview programs.  Then, I would compile it, and put a Open Reference, Read/Write, Close Reference, in the RT VI.  And.... it doesn't work.  Obviously, I am doing something wrong. 
Can someone teach me how to do it?  It would be rather crazy to try to fit all 96 DIO controls into one top-level FPGA VI.  Thank you.