You can do similar adjustments using the same graphs jtaldon and I are talking about in that thread if your sub has controls. However, your sub MUST have speaker in and speaker out connections and you should have your speakers hooked to these.
For example, time delay on an AVR is equivalent to the Phase knob on your sub. Some subs have just a 180 degree switch. This made a difference for me in time aligning my subs even though my polarity was correct! I also changed the crossover slope of my subs in that thread, but most subwoofers don't let you adjust the octaves/dB slope. Note that sometimes you need to subtract from your sub's time delay; in this case you would have to try putting the subs closer to the listening position. The phase knob isn't psychic so it can only add delay to the subwoofer's output.
To be honest, this is a little complicated the first couple times you do it. I would start by doing some baseline measurements and studying them. Even if I had no phase knob, I would still experiment and try swapping sub polarity and moving the sub closer or farther from the listening position as needed.
One thing to think about is if you want room correction with the Oppo HA-1 is to use the Dirac software (stereo version). If your sub(s) have speaker in/out connections it is worth using those as Dirac would do a decent job time aligning everything for you. This is because the stereo signal would be processed by the Dirac software then go through the sub, then to your loud speaker. Yes it will have to do extra processing, and you would/should turn it off when using headphones. Definitely the Dirac room correction is for speakers only. Dirac does a wonderful job fixing impulse response issues, something that can't be fixed by traditional EQ (but can be fixed via room treatments too which is a passive option to consider).
There is also the miniDSP option for bass management, but it would mean putting another device in your signal path. Honestly, getting good bass requires at least two matching subs of decent quality. I would really spend my money and time on that and doing measurements with REW before ever trying room correction. Also, plenty of other options such as bass traps and absorption on the walls, outboard analog crossovers placed between your HA-1 and amp, etc...
I understand most audiophiles are purist and against room correction, but the Dirac software will improve the imaging of your speakers and will likely improve the time alignment.
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Thanks etc6849, but looks like they're talking about using an Emo HT processor to apply correction. I had thought you were using just the HA-1 to time align your mains and subs and was wondering how this was possible without an additional piece of hardware.