Need help with the format of rpd files and EPCS64 chip

Well, I'm using a cyclone II chip with an EPCS64. I'm considering configuring the FPGA chip in a particular way. But I am stuck at a problem.

The problem is that I'm not aware of the format of rpd files. Is it possible to let the some of the inputs fixed on some logic values by editing the rpd files?

More specifically, my purpose is to configure the FPGA like this: the inputs will be fixed on some values (for example 0001) for one second, then changed to the other value(for example 1000) for another second. In the end we don' control the input ports. The value of inputs depend on the real inputs towards the circuit. I wonder if I can do this by editing the configuration files loading into the EPCS chip. Or is there any alternative way to do this?

The description might be vague. Any suggestions or ideas will be helpful!