If I only have a tape measure, I use that to start with.
If I only have an RTA, I will use a technique called "nulling" where I flip the polarity of one speaker and then adjust time alignment so there is maximum cancellation between the two speakers (largest null in the RTA).
If I have a dual-channel FFT system like SMAART or OpenSoundMeter, then I use the phase response directly.
After I get close using the tools, I will fine tune by ear using the technique below. If I have tools then this process is much faster and I can match phase over a larger range of frequencies and use other corrections like all-pass filters which I find difficult to do by ear. If I have no tools available, then I use the technique below but it takes a lot longer.
To fine tune, I will set the lowpass filter to somewhere around 200hz and play only bass. I will play a mono track with a male voice like the introduction tracks on the Chesky Ultimate Demonstration Disc. I set the time delay for all speakers to the middle of the range on the equipment, like if the maximum delay per channel is 10.0ms then I set delay to 5.0ms on all speakers. I choose one speaker as the time anchor, usually front left woofer. Then I'll close my eyes and listen to a pair of speakers and adjust time delay until the mono sound appears to come from the "center" of the speakers. I will also check polarity by flipping the polarity of one speaker and ensure that it sounds more focused or not.
There are always cases when I give up "perfect" time alignment. The two most common are when a customer wants the sound to be more enveloping or surround-sound instead of precision focused in front. The other case is when I have a rear speaker that is very close to the listening position (like a rear speaker in an off-road vehicle) and the sound appears to be coming from that near speaker only. I will adjust the time delay of that nearest speaker slightly so that the sound stage moves away from that speaker and appears to be more balanced with the other speakers in the vehicle. A good example is the rear speaker in the Polaris Slingshot, where the rear speaker is directly behind your head about 6 inches away.