So the answer is to generate the NGC files by making the modules you want "the top module" you can then run the synthesis to generate the individual NGC. Then proceed as normal when adding IP to a PCore. So adding these NGC files to the netlist folder and modifying the BBD file and all that!
As a note for completion to get the module working you need to set the synthesis setting "Xilinx Specefic" -> and disable "add io buffers"