Don't wory about it
Your current method of hooking up the sub is the correct way since you have a sub out. You would use the speaker level inputs on the sub if you did not have sub out on your receiver, or receiver had no bass management and you need to use the sub high pass crossover.
The two sets of connectors are there to allow the speakers to bi-wired or bi-amplified if you were to defeat the internal crossover. Bi-wiring is pretty much pointless and bi-amping requires the use of external active crossovers. As long as there is a bar, known as a jumper, connecting the upper set of terminals to the lower set of terminals it doesn’t matter which set you have your speaker wires connected to.