though a lot of subs will have the "left" designated as LFE for some reason.

If you want, you can buy a y-splitter to plug both, but that doesn't do anything. You'll get a 3db boost, but you can do that already by turning up gain. So if you use splitter, lower the gain.

re phase, you'll have to use your ears, or a test disc of some sorts. Or more advanced stuff that will easily show you on graph.

If its a simply switch, not variable, I presume its either 0 or 180 deg.

You'll have to play with both. It may be too subtle for you to discern, but the better phase setting might sound a bit louder or fuller...