Im not sure I understand where/what your problem is
If you can communicate successfully to the micro-controller with Hyperterm, then, in your GUI app, surely all you need to do is
a) open up a serial connection - see here
http://msdn.microsoft.com/en-au/library/system.io.ports.serialport(v=vs.110).aspx[
^]
b) set the serial connection to various speed, bit, check parameters
c) for a 'setting' on the gui, transmit that using the serial connection
d) read the result back from the serial port
Part (a) depends more or less on how your serial connection is plugged in - you may be talking through a USB-serial bridge for example
Using Hyperterm is a good option - that with the documentation for the microcontroller should give you the parameters for (b), and your manual testing and (again) the microcontroller docco will give you the data you need to write at point (c)
I wouldnt even start with a GUI if it was me - I'd go from Hyperterm to a console mode prototype then to a GUI
'g'
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