XBee transparent mode with Alternate pins.

SoftwareSerial mySerial = SoftwareSerial(2, 13);
mySerial.begin(9600); // Setup Serial library at 9600 bps

Do you really have a mySerial connected to these two pins? Use a meaningful name!

The SoftwareSerial instance is local to setup(). When setup() ends, the variable goes out of scope. You won't be able to use it in loop(). Sort of makes it useless, don't you think? A global instance would be a lot more useful.

I then hooked up one of the XBees to the Arduino using pins 0 & 1 (RX & TX) and the code worked flawlessly

Good.

But I can't for the life of me figure out how to get the RX and TX to move over to pins 2 & 13

You have to move some wires. Unless you are using a shield to connect the XBee, in which case you probably can't use pins 2 and 13.

much less both serials to work in the same code (The end goal).

Well, first you need to get the XBee connected to different pins...

If the XBee is not connected to the 0 and 1 pins, that code is going to do nothing. You need to read from the serial class instance that owns the pins that the XBee is connected to.