How to access FPGA Manager's Input & Output ?

I is the programmer, in principle circuit don't know !

May be method to insert your code in HWLIB-example, where LEDs was blinked -- there buttons MUST be available!

And then cut small portions of big code, try compile and run -- while buttons may work, else undo cutting, cut another lines... In that way you get minimal program and understand, what current is bad. While not finded good documentation :)

P.S. Try .svd files in debugger, as described in ug_soc_eds.pdf -- your code not need, and all GPIO may be visible after init.