No, there's no way to skip around in an automation track. That's on my wish list and I'll add a vote for you.
If you put your MIDI messages into Standard MIDI File and attach that to your recording, then when you skip around in a recording, the SMF will move with it. But that would require that you do all your MIDI programming in another app and save everything into a file, instead of using BandHelper's own system of MIDI presets and attaching presets to songs.