How should i connect my lipo battery to the proffieboard? I’m using this battery
The battery also powers two step up converters. Can i take the pos of the battery and wire it to the BAT+ and the neg of the battery to the BAT- on the proffieboard? I also want to be able to charge the battery while the board is plugged into the a serial port.
li-po and li-ion batteries are basically interchangeable.
This page generates circuit diagrams:
https://fredrik.hubbe.net/lightsaber/v6/configurator.html
Do you have a V3 proffieboard? If so, the battery will charge when USB is connected.
Does this just work on the v3 without any kind of setting up or config tweaks?
How did I miss that? LOL! Great to know. 
Yep. No settings or configuration needed.
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Yes i have v3.9 board. So i do not need an external charging circuit? The battery is connected to two step up converters, one for powering the 12v LED strip and the other for powering the dc motor. Can the onboard charging circuit handle that?
The charger only provides ~450mA. If the step-up converters (and everything else) draw more than that, then no charging will occur.