Hey dllcm, all these questions are referenced in the user guide for the P1, but I'll touch on each one briefly.
The battery charger has numerous settings, which ones do I need to use?
For the Balance Charger BC20-4, the left slide switch should be set to LiPo. The right switch, if you have a stock 2200 mAh battery, should be set to 2A. If you have a third party battery, like a Multistar 4000 mAh, then the highest setting of 3A should be used. A rule of thumb is to match the battery amp rating (mAh x 1000 = A) with the setting on the stock charger. Those are the only two settings on the stock charger. Be sure to plug in both cables, the XT60 connector and the small white four conductor, which goes in the 3S jack.
What is the usb cord inside the shell for?
The USB cable located in the battery compartment, allows you to connect the Phantom to your PC in order to change/verify settings in the NAZA M V2 Flight Controller and perform various calibrations. It's important also to download and install the appropriate drivers from the DJI website before connecting the bird. Some of these settings and calibrations should be carried out before the first flight.
When I lift off the the led starts flashing ready, is this due to a low battery?
If you are referencing the Flight Status LED on the rear of the bird, the flash codes are in the user guide or available online, as well as in numerous threads here on the forum. We would need more specific info as to what color and how many flashes to diagnose the status. It's a good idea to never fly with a battery that has not been fully charged.
I hope that answers most of your questions or points you in the right direction to gather the information. Being prepared with all the info before the flight is critical to safe and rewarding flying. Have fun and fly safe...