Right. When the patch is running on Bela you cannot access its GUI or edit it. So you'll have to do the editing on your computer.
Maybe the best approach is yet a different one: you could import your audio file in a DAW (e.g.: Reaper), create an extra track where you draw MIDI automation. Bela can receive MIDI from the host via the USB cable and turn it into analog outputs (check out the
PureData/midi-cv-midi example). In this prototyping phase, you'd be playing your audio out of the host computer and the CV out of Bela.
Once you are done prototyping, you'd export MIDI from the DAW and make a Pd patch which plays back time-aligned MIDI + sound (for Midi you'd need MrPeach's
Does that sound doable?