If you use the proper JST battery connector for the battery then you're sorted. You can power by USB on any battery.
You can connect your battery to BAT on the pin headers and power the board via USB, but only if the battery voltage is above 4.3v. If the battery voltage is below 4.3v then you'll end up charging your battery to 4.3v from USB at currents up to 1 amp (which is probably not good for your battery or PC).
If you use the pin headers to connect the battery and you get the polarity wrong then it'll probably break your board and anything connected to it - so be careful! The proper battery connector has reverse voltage protection though :)
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
Glad it's working!
Just to clear up about Battery/VBAT/USB:
There's some info here including the circuit if that helps: http://www.espruino.com/EspruinoBoard
In short: