HVAC Wiring: Any reasons for one zone to be wired different from others?
These are all AC voltages. Basically, you have a transformer output, a thermostatic switch, and a motor driver (actually a relay) all in a loop. It doesn't matter which order the three items are wired, so either of your two wiring plans should work fine. (I presume that your heating system has been working fine.)

The only reason to regularize the wiring is to lessen confusion in the future, which is a true benefit, but since you have this quite clear diagram it would be just as valuable, and much easier, to just post it by the furnace.