Choosing your 'delay points' in the room is always a compromise; delay changes relative to the distance from each speaker, so you must choose the position at which the delay is most audible, i.e. choose the point at which both speakers are heard at equal loudness. This is the acoustic crossover point (nothing to do with frequency, and no relation to the crossover DSP or circuitry in your system). This is the point at which any errors in alignment will be most clearly heard, so the alignment should be done here. As you move further away from this point, becoming closer to one speaker or the other, one speaker will tend to dominate and eventually mask the quieter one.
Note the implication that this has on speaker positioning - simply swiveling one speaker on its pole by 20 degrees might have a drastic effect on this crossover point, potentially moving it by several metres and putting the system out of alignment. Level changes between speakers made after time-alignment (e.g. turning the front pair down to combat a lively lectern mic), will have the same effect.
So there is a natural order of tasks in aligning a system: 1. Position the speakers in the right place, 2. Set the splay angles to achieve the coverage you need, 3. Set the relative levels between speakers. Once you're happy that the system is covering the area nicely, you can, 4. Find the acoustic crossover points and carry out the time alignment. After this point, do not adjust the relative levels between speakers, and do not move or turn the speakers. Doing so will mean that stage 4 will need to be repeated.
You don't need an expensive measurement system to do the alignment; you should be able to find the crossover points in the room using your ears: mute the speakers that you're not interested in, play some music and stand at the point where the two speakers are the same loudness (technically this will be one of any points along a straight line, but use your judgement here). Measure the distance to each speaker and subtract one from the other to find the path difference (a laser measure is a useful tool for this). Set the delay on the closer speaker relative to the further speaker to be the time value that corresponds with this distance measurement. Let your ears be the final judge - play something with obvious percussive hits, like a click-track or metronome and make sure that the alignment sounds correct, tweaking the delay if needed.
I think you will find that your delays end up being a fair bit shorter than your present values.
You might then consider delaying the whole system back to the stage, but that's less of an exact science and its effectiveness is debatable.
As for the sub, it doesn't make sense to time align subs to mains - phase-alignment is the technique you should use (group delay means that some frequencies can arrive 20ms or so later than others, depending on the particular design of the sub), and to do this correctly requires a measurement system such as SMAART or Systune. Then there's an argument of what point in the room to phase align at - it won't be possible to have the sub and top in phase alignment at the crossover frequency at every seat in the house - probably far from it, so it's largely going to be a wasted effort, especially in a small venue such as yours where reflections and room modes will likely come into play.
