You should gather some information about your current HVAC system before you do anything. Stuff like how many CFM its moving, static pressures, and a map of the existing ductwork.
Is your current HVAC system even working correctly? How do you know that ? Oh, some service guy that didn't graduate from high school told you so? Remember the Dateline NBC expose (that's ex-po-zay) where they were sucking refrigerant out of a properly charged system? Learn about your HVAC unit and check what you can. At the very least learn where your indoor coil is and clean it. Check your ducts, seal any leaks, insulate if appropriate.
You might even want to have somebody reliable run Manual D's and Manual J's on your house to see how its performing now to give you a staring point. I think there's some fairly cheap software you can buy to do them yourself. That's another thing that ticks me off about HVAC; the Manuals which contain the formulas for the calculations are not public domain. They are developed and sold by ACCA yet the building authorities require the calcuations. That's a self serving closed loop society.
I checked out the sourceforge link. Didn't read the whole thing yet, but it looks like they cover a lot of theory and how to in the FAQs. DZ (the software) is written in Java. Personally I hate Java but that's another topic. Download the source and figure out how it works. You'll just need to apply it to your own situation. Its not a one size fits all.
2) there are no local thermostats--all the control is in the PC.
I couldn't find that specifically, but I'll take your word for it.
For a conventional looking approach, what I would try is a non programmable digital (for accuracy) thermostat in each zone. Supply 24vac to each thermostat. When a call for heat/cool occurs, have it close a 24vac coil relay whose contacts can then be sensed by the contoller. I'd have the 24vac xformer and relays near the controller and home run regular thermostat wire to each one. You'll need to use two (or three to detect fan) inputs for each thermostat.