I am not enough skilled to solve the Battery/USB cabling to have teensy alimented by usb or battery and communicate with the PC with USB (when needed)
With option two, just need solder the boards..
OK, here's a "schematic" how to connect teensy 2.0 + extra board (e.g. EZ-key) with the LiPo charging unit (e.g. Adafruit Lipoly backpack) and diodes, so that
1) if USB is connected, everything runs from the USB's 5V and the battery is charging
2) if USB is disconnected, everything switches automatically to battery
Drawn schematic pictureThe stuff that needs to be added to the existing boards is in red. You'll need to cut a trace on the bottom of the teensy (to disconnect USB's 5V from teensy's VCC), just as described
here. One wire from the teensy will go from the "5V" = "topmost" pad on the bottom of the teensy, and the other one from the normal VCC pad on the side.
The point is that the diodes only allow current in one direction. So if USB is connected:
a) teensy's VCC and EZ-key's VIN are at 5V level from USB
b) the diode between "BAT" and VCC/VIN prevents the current from flowing back to the battery
c) the charging unit's 5V is also connected to USB, so the battery is charging.
If USB is disconnected:
a) teensy's VCC and EZ-key's VIN are powered from "BAT"
b) the other diode prevents the battery output from going back to 5V on the charger
It may be a good idea to throw in a couple of 10uF caps to make the voltage changes smoother, in case connecting and/or disconnecting the USB cause some trouble with the teensy or EZ-key, like resets.
By the way, this is exactly how is it done on Bluefruit LE Micro, Adafruit Trinkets, etc... I just looked at their schematics and they exactly just use two Schottky diodes like this. The only extra step that's needed is cutting that trace on the teensy.