How Do I Adjust A Subwoofer For Best Sound?

Your 6.5's will likley "roll off" at a certain freq, so a filter may not be necessary at all*.

What does the crossover control say?

If the 6.5's will do 60 Hz, then technically setting the sub crossover at 60 would be "correct", however, your ears will tell you what sounds good.
You really need the actual spec of that 6.5" speaker to use as a starting point, otherise, just set to what sounds good to you.

*Putting in a hardwired filter before the 6.5 could theoretically creat a "hole" btween the 6.5 response and the sub response.
That's not necessarily a deal killer, but something to be aware of.

Personally, I like a hard 60Hz hit. It's a good sound for "rock and roll", and some electronic music.

If the "phase" is cancelling out frequencies, you should be able to hear that, and set it accordingly.
I've never seen an adjustable phase switch. Like above, they are usually "in" or "180*".

As you move the sub further away (like in the trunk) the increased time it takes for the sound waves to get to your ears could cause it so sound "out of phase" with the other speakers, cancelling out some frequencies. It certainly could compensite for the sub being wired incorrectly, but that's not the actual intent.