Do what the pros do: Use a visual/audio cue.
Ever seen a TV show about moviemaking, where someone steps out with a clapper and says "Take one" and then claps the clapper shut? That's what he's doing. Creating a visual cue that will give the sound editor something to sync to.
Having someone on-stage give you a clap is the easiest way to give yourself a visual/audio cue. Otherwise, you'll have to improvise, trying to match up a drum smack or guitar chord change, which is a bit harder.
Agree in advance on some visual/audio cue that creates a quick pop or smack that you can see on the audio track's waveform and the rest will come easy.