Yes you can still use the sub without sub out put by having your receiver go through the sub input and out for your floor speakers,bookshelf speakers or cube speakers. This sub woofer is amazing in deep base due to its built in EQ
Since it is a passive sub it usually has a built in crossover and that it is powered by potentially a stronger current from your receiver, since this polk does not have an internal crossover and rather an actual one on the back side of the sub it is entirely possible to be wasting watts on high notes that it doesn't even need to be going through it. The easiest way to determine this is to play music will medium to high vocals in it and to put your ear need the speaker itself and not the port (all you would hear is air and bass) and to fine tune the crossover till you cannot hear a single note of vocals. I have used mine with all types of music and i can guarantee it that a 6.5 shouldn't be as loud as this one. It was literally shaking my friends walls across the house and it wasn't even turned all the way up. The bass from this isn't clean, however and if you want tight punchy bass then the 6.5 will be more controlled, but if the 6.5 is just all around louder then it must be a defective unit. I've done car audio for many many years and unless the 6.5 has about twice the magnetic weight and about twice the power it shouldn't be louder. Pioneer isn't really known for their loud subs either. Make sure you are testing the two units in the same exact spot as well and readjusting your receiver settings before each test as the settings for the 6.5 shouldn't be the same for the polk.
Connecting both Sub outs is not a good idea.
You have 2 choices:
1. Connect 1 Sub out/LFE to either the Left or Right input on the sub using a single RCA cable
2. Connect 1 Sub out/LFE and use a RCA Y splitter to connect both Left and Right input channels
You MAY hear an increase in output using option 2 but that is also what a volume knob is for.
I don't use it in auto mode, i have mine powered from the reciever it only goes off when the reciever is turned off. try running the power with an extension cord if needed to the switched outlet on your reciever .