I know the function and am actually certified for air conditioning but the engineering part I know just enough to be dangerous. The key to proper function is calculated flow. The fan size, speed and what not is calculated for a specific target CFM of air flow at each vent. They may change duct sizes along the path to change flow or restriction or to manipulate the pressure at each vent. When they add on to a system, they rarely add flow to it, just volume of duct. Putting in fans to move the air along only works if there is enough restriction to be overcome to make that flow valuable. Most of the time, it isn’t. You can do some manipulating of the air handler itself (the body of the heater/air conditioner) like variable speed fan drive (VFD) to speed up or slow down the fan to control CFM but that is only good if you have a way to throttle the hot or cold output of the guts of your handler. Again, not enough air flow, overheat the hot parts or freeze up of the coil for a/c. HVAC is not something that you can really easily tweak up or down. These systems really need to be changed from the ground up to have total control of their function. Not saying you can’t play with it as they are not hyper sensitive but as you do play with it, keep an eye out for the effects those modifications are having on the handler. The hot side is not quite as sensitive as the cold side (if you have a/c as part of your handler).
Basically, the box is designed to do (x) cfm flow wide open. Each vent is calculated at (y) cfm flow wide open. The totals of the vents needs to be roughly the same as the flow of the box (x=y). There are also ducting restriction calibrations in that as well but they are not huge unless the ducting takes lots of corners or has lots of small feeder ducts from the main. You can close down a couple and still get acceptable flow. You can’t however auto-vent everything and let them control room temp. The fan will always blow the same speed unless it is a VFD and way smarter than a normal residential handler. You need to make sure your box temps in the handler stay close to what was designed with all the vents open after you have made modifications. And remember, you dont have temp readings and compensation in every room unless you put it there. Cycle times are important too. If you have electric heat in the handler, that can be turned on and off instantly. Gas or oil heat has a cool down time that has to be considered. That creates temp swings in small spaces.
Hope that helps