John,
You will have one IAK file, it will have one Comm Resource (by default, "FP Res", 12 devices (1 network module + 2 IO modules per bank * 4 banks) and ~84 items (channels). Each FP-1000/1001 module will have it's address as a multiple of 10 (0, 10, 20, etc...) and the module attached to it will be addressed as the network module address +1 (for the module directly next to the network module, +2 for the next one). The FieldPoint Server is designed to allow multiple client programs to link to it at the same time. In this case, each of your client programs will be addressing a different set of modules, but they could also access the other modules.
Regards,
Aaron
LabVIEW Champion, CLA, CPI