Motion control problems

Hello i am a newbie engineer in my first month and i am given a PC/104, an FPGA based motion controller, and H-bridge, a servo motor and an encoder; and i am asked to design a motion controller system.
Anyway the point is, i am trying to program my motion controller with MS-DOS based program however, i cannot have any motion till now.
I am asking help from people who have experience on motion control -or even FPGA based system design- i can give more details if any of you will be kind to answer.
Thanks a lot
Alkim

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