I asked erv about this some time ago as I knew I was going to do a NB build. Actually, wiring your accent LED to the 3.3v pad will work with out the need of a recharge port. At least that was my understanding.

Darth Ryo is right in that the LED will stay on and use the battery unnecessarily while the board is powered. However once the board enters deep sleep mode (which btw is a configurable value of the board) the LED will power down as well. That's the whole point of the deep sleep mode delay of board. It's a power saving mode that allows the battery to last longer on one charge when not in use. IIRC when the board is in deep sleep mode, it uses less than 0.1mA. It's meant to act just like a kill key.

So the only question is what kind of look are you going for. If you want the accent LED of your switch to be on whether or not the main LED is on, the wire it to 3.3v pad. If not, wire it in parrllel with your main LED.

It's also important to remember that accent LED's don't draw much juice (depending on what resistor you use). I prefer mine to actually under draw current a little bit as I feel that accent LED's should be just that....accents. I want to be able to see them but not be blinded by them. Especially when you're considering using green, white, or blue as they can be insanely bright when giving the juice. Green and white just love current. A 10mA draw on an accent LED will hardly bother a 2600mAh battery.

Your other option is to always make it so your battery is removable.