From what I understand, the realign function should only be necessary if you are getting out of sync with the clock. That can happen if the clock timing isn't consistant enough. It locks onto the timing when you start your clock but then it can drift apart. It is supposed to realign itself though. If you have feedback set to anything other than 100 or you are in overdub mode for a while, they can drift and you can force a realign. At least that's how I remember it.
Wait until a half a beat before the end of loop 1 to switch to loop 2. You are probably set to be quantized at a duration that is less than the duration of loop 1 so if you switch too early, it will switch at the next cycle. Always trigger the change just a partial beat before the end of the cycle. If you try and do it at the cycle it's easy to get it too late and then the timing will be screwed up. If you do it too early, you may cut off your first loop.
Glad the pedal advice helped. If anyone knows of a better MIDI pedal to use with the Echoplex, I'd like to hear about it too.