I have a Dayton Sub. It has more then one input. It has two plus and two minus inputs which one do I use. I was thinking of using a y connector from the receiver (onkyo 605) since it only has 1 input.

You are probably looking at the speaker or high level inputs. These are for connecting to speaker outputs. You should see left and right line or low level inputs (they may also be labeled LFE In or Sub In). You connect either of these to the LFE or Sub out from the Onkyo using a single RCA cable.

If possible, you want to use the RCA Line In jack to the Line Out on the receiver.

It is labeled LFE on the Onkyo 605. Connect that to LFE in on the sub.