It is not that difficult, but unfortunately Xilinx documentation is not that clear.
What you need to do after you are done with your Microblaze code and you feel comfortable with it, is to create a new project in ISE or the one you already had, then add a new file to the project, but instead of adding a VHDL or Verilog file, you must add the system file from EDK.
After you added your XPS project into ISE, you need to do some manual work in order to make things work for you.
Here are a list of things that needs to be done:
- You have to create a UCF file that includes all the constraints from EDK
- You have to make sure that you have enough space inside your FPGA for both the EDK and your own code
- Synthesize and implement your design using the project in ISE.
- Program your FPGA from the bit file generated by ISE
In order to communicate between the MB and your own code, you can do it in many different ways, the easiest way is to use the GPIO block from your MB, then connect those signals to your own code on your top level wrapper.
You maybe able to find some useful information on the lab document and lab material from the following Xilinx page: enter linkXilinx EDK interface class description here
Accessing the GPIO is pretty simple, you can use the information on this page to get you started: Reading DIP Switch with MicroBlaze
You may also find this document and related files very useful, it is not for your board, but it covers the exact same thing you are asking for: Avnet MB tutorial document
I hope this is clear enough.