a problem about programming into developementboard

my development bord is apex20k and the fpga is ep20k200efc484-2x.in my design i have assigned the jp12 and the jp11 as my expanded interfaces.however,when i downlaod a c program into the fpga,it has't run as my expectation at all.i have used the excalibur head file,and created the s-record file very influently.i don't know where the problem lies.

so my question is:when all the pin on the expended interfaces have been correctly assigned,and want to send a high level to a specific pin eg jp12 pin2.how should i make it and how to write a c program file to realize this function.because i suspect my c program is not matched to the interfaces i have assigned.