Thanks Dana, that did help. (I am having issues with the miniprog hence the delayed response, it sometimes just doesn't want to program anything).
So now I have control over the memory I am trying to figure out how I can calculate where the code would reside in the PSoC flash. I have a defined location in the memory for the emEEPROM (0x1a00), but I am not sure how to erase/program the flash blocks up to that address.
Additionally, the application note said to change the customer linker file to tell the design to leave that area alone, but as I have a defined memory location (on the command line link function) I should not need to do that correct?