Hmm, not totally sure, but the dedicated line may have been for a pressure (return) side cleaner. I am not even close to an expert on cleaner equipment so I will defer to those ppl. That being said, this line:
It also seems to make one of the water outlets lose its prime and push out water softer.
Makes it seem like the pump is not drawing enough water through the skimmer when that cleaner is hooked up.... you are submerging all the hose before hooking it up to draw out water right? Also, if you have an adjustable valve, if you close the main drain so it is 100% skimmer do the returns seem normal?