OpenCL guidelines to use physical pins of fpga

For mixing RTL with OpenCL, check "Intel FPGA SDK for OpenCL Programming Guide, 2.1 OpenCL Library". There is no documented way of generating the OpenCL project, modifying it, and feeding it back to the compiler as you want. Doing so will very likely fail or not give the intended results.

Adding I/O interfaces to the project will require modifying the BSP, and generating a new one. The main document outlying this process is the same "Intel FPGA SDK for OpenCL Custom Platform Toolkit User Guide" you mentioned earlier. That involves a lot more than just modifying the board_spec.xml. You must generate all the necessary IP cores and write all the HDL code yourself to define a new I/O channel to access the specific I/O that you are trying to add, and recreate the BSP. After that you can access that I/O interface from an OpenCL kernel using the I/O channel that you defined.