I think I understand what you are trying to say...
First, turn off the breaker that supplies power to the switch panel for the fan. Turn all of the switches in the fan switch panel on to make sure there is no power to anything. Remove the two fan switches completely. Connect each wire seperately to it's other same colored wire. The wiring will then be wired direct to the fan with no interruption. Put a blank panel up where the switches were, turn the breaker back on, and you are done. Your new fan will come with a relay or some sort of control box that will control the fan.
If the wiring coming from the source is a different color from what is going to the fan, do not play guesswork. Take a clear picture of it all and post it up here or call an electrician. I think I covered everything. If not then someone post up.