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Originally Posted by ImmortalAres
however there are a lot of function prototypes in the start up file (ifi_startup) that i can't find code for ie the ifi_intialization that apparently "Configures registers and initializes the SPI RX/TX buffers." which seems important to me
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It's probably just a call to some master RC stuff. (as you assumed) According to what you said, it sets up the registers on the processor, so if you have any low level direct register stuff, you'll have to fix that, and it initializes the input and output buffers.
What fowlern said is basically correct. The master processor just sits there and receives all outside data. (from sensors, controls, etc) It then handles if appropriate (for instance, the disable signal) or passes it along to the user processor. For most output, the user proc sends it's desired info to the master and the master then sets things correctly.
The way it's setup is great for you because all you have to do is create some wrapper code which takes care of simulating the data transfer between your code and the nonexistent master.