Hi Peter,
I'm new to beaglebones but not lipo's.
Your batteries may have 2 connectors.
1st is the usual power connector, it has just 2 wires and could be any type of connector. It has the total voltage on it and should be about 4 times the number of cells in volts (i.e. 2 cells = 8 volts) approx.
2nd is the JST connector, there should be 3 wires for a 2 cell battery. Thats ground or -, the centre tap, and +. Ground is usualy Black and + Red. This is normally the balance connector. The voltage between Red + and Black - should be as above and - Black to centre tap should be about 4 volts and centre tap to + Red the same.
JST connectors are hard to get a good connection, be VERY careful not to short the terminals together as this is almost always the end of your battery and can be dangerous from a fire point of view. Make sure your meter is on Volts NOT Amps and that the leads are in the Volts position. Lipo's can be risky.
It is still possible to get batteries with odd configurations, 2s2p and similar tell you about the way the battery is connected inside.
The s is for serial and the p is for parallel. These are unusual now for hobby use.
Best Wishes
John.
If I'm telling you things you know already, sorry!