my sub has a left and right input. should i use a y adapter to connect my sub or should i just pick one to connet my sub cable to? does it make a big difference if i use a y adapter?

You should be fine using only one cable.

I have a HSU STF-3 with L and R inputs. I tried using a Y adapter and could not detect any difference in output using an SPL meter. I also have no problems with auto power on using a single cable.

The only reason for the left and right inputs (AFAIK) are for systems without a dedicated sub output that have line out ports (or integrateds with jumpered RCA jacks between the preamp and power amp where you can insert Y adapters between the L&R channels and the power amp. A full range signal gets sent to the sub and you'd use the sub's crossover.

The signal received by both ports is summed, which should have a net zero effect as you are sending the same signal to both jacks then summing them.

Hope this helps.

Do you have a user's manual for your sub? What does it say? If you don't have the print version, perhaps there is an online manual you could find.

In general, using a Y-connector on the input has no advantage in many cases, and in a few cases would be detrimental. If you have no specific official information on your subwoofer, just use the input labeled for the left channel.

Agree with palmer and BB4TB. Let me add that, if you use the Y adapter to send L/R channels to your sub, you will need to tell your preamp that you have no subwoofer. Otherwise, in cases where you have a dedicated LFE signal, your sub won't be seeing that. One difference of this arrangement is that you would solely rely on your sub's crossover settings, unless of course you have something like a SMS-1.
IMHO, the single cable from your "sub-out" to [usually] the left input on your sub is the preferred method.

Garcianc2003's comment about turning the sub off in the receiver or processor is assuming that you use the Y adapters to send copies of the left and right front channels to the sub - it does not apply in the case of splitting the subwoofer output and connecting it to both inputs on the sub.

I've simply connected to the left input on both my old sub (SVS 25-31 PCi) and my current sub (LFM-1).