Setting up the Align ESC is not overly complicated but quite confusing if you don't know what all the beeps are about.

The following is a description in words of the setup procedure, bear with me as it is quite complex to explain.

Firstly your tx must be setup such that your throttle curve is the default linear curve. ie. 0 25 50 75 100 for a radio with a five point curve. The reason for this is that the ESC uses the stick position to sense what settings you want during the programming phase.

Next step is to put your stick at full throttle and plug in the battery (yes, I was also worried).

The ESC will emit a scale (crecendo) of notes in quick succession indicating setup mode being entered.
Put the stick at low throttle and the setup sequence begins.

The ESC will now emit a single beep, repeating slowly, this indicates option 1 is being set. Put the stick in the appropriate place for the setting you want. Option 1 is the break setting, so should be turned off in a heli, so the stick should be at low throttle. The ESC will wait a preset period of time beeping once slowly and then take the option as wherever the stick currently is placed. If you are following these instructions then you won't have moved the stick from the low throttle position at the start of the setup sequence.

The ESC now emits a scale of notes in quick succession to indicate the setting has been taken and will now beep twice, slowly and repeating. You are now setting option 2, hence the two beeps slowly repeating. You are now setting the timing for the motor. Place the stick in the appropriate place for your motor. Option 1 is low timing, option 2 is mid timing and option 3 is high timing. For an Align motor mid or low timing can be used, so middle or low throttle for the stick.
After a preset period the ESC will emit a scale of notes in quick succession, indicating the option has been set.

Following this the ESC will emit three beeps, repeating slowly, you are now setting option 3 for battery protection.
Again place the stick high, middle or low. I set my battery protection to high (70%) which is the low throttle stick position. This gives you just under 9v as the point your ESC will enter battery protection mode.

After a preset period you get the scale of notes in quick succession and then the ESC plays back your settings using beep codes for option 1, 2 and 3. Listen carefully to verify they are correct.

If they are then unplug the battery, plug it back in and go fly. If they aren't correct unplug the battery, place your stick at full throttle and plug the battery back in again to re-enter setup mode.

I hope this makes sense, it's very hard to explain, I may make a video of it with commentary at a later date if I receive feedback that this is too hard to follow. Let me know on the TrexTuning forums.