If both 2- and 3-cell packs are same capacity, manufacturing, and charging/discharging history, they may well drain at approximately the same rate.
But personally, I do not get why you would not use the 5v from your speed controller BEC. That one will, if properly configured, always give the power needed by ArduPilot, Rx and servos even when there's not much left for the last landing approach. If it is for engine battery monitoring through telemetry, then I understand.
You could then as well just monitor a single cell (or 2 or 3) through the balancer connector to get an estimation of total capacity left. On that connector, black wire is GND and from there, every next pin accounts for one more cell total:
- GND and first next pin: 1 cell
- GND and second next pin: 2 cell
- GND and third next pin: 3 cell
With some basics calculation, you get the total capacity left.
I'm sorry, I should have gone into more detail. Yes, both packs will be brand-new, 5300 mAh ElectriFly LiPOs, and yes, I am looking to monitor the batteries via telemetry. The EzOSD voltage detector I'll have in line will display some critical battery information, but I'd like to have some redundancy built in.
At this point, I plan on powering the video system / OSD through the 3 cell LiPo (which is in series with an identical 2 cell LiPo to power the NexStar) so I'll check back later if I've got any questions.
Thank you both for the help, I really appreciate it.