Trouble Using Input Shield and XBee

Hey, I am trying to make two Arduinos (Arduino Mega1280) communicate wirelessly using the XBee. The XBee shield I am using is here http://www.liquidware.com/shop/show/XBS/Arduino+XBee+Shield. I have been able to get two Arduinos to communicate via XBee, and I have been able to verify the functionality using LEDs. I start having problems, however, when I try to use this input shield http://www.liquidware.com/shop/show/INPT/InputShield, which has two buttons and a joystick. I have been able to get the A and B buttons to work, but as soon as I even write code that utilizes the joystick I cannot get the Arduinos to communicate at all. When I plug in the “sending” Arduino (the one with the input shield) up to my computer using a usb cable, my computer sees the write serial output. However, the other Arduino cannot receive the message wirelessly. I think the problem might be that the input shield shares some pins with the XBee shield. Specifically, the XBee shield uses the pwm pins 0-7, as well as the analog-in pins 0-5. The input shield plugs into every single pwm pin available (0-13 plus the Aref and gnd pins above them), and also plugs into the analog-in pins 0-5, as well as the reset, 3v3, 5v, gnd, and Vin that are directly above the analog-in pins. Note that the shield I am using has an A and B mode, and I am currently using B mode. Do I need to find a way to separate the pins out so that the input shield and XBee shield are not sharing pins? If so, what is the best way to do this?
If I need to clarify anything, please let me know. Thanks for your help!

Specifically, the XBee shield uses the pwm pins 0-7, as well as the analog-in pins 0-5.

First, not all the pins from 0 to 7 are PWM pins. Second, the shield does not use all the pins. It simply has a header that passes the pins to the top. The shield only actually uses digital pins 0 and 1.

How are you attaching both of those shields to one Arduino? Which one is on top?

We had the input shield more or less on top of the XBee shield. It's actually all on a breadboard right now. Unfortunately, I cannot see that breadboard until Tuesday. In the meantime, you said that the input shield doesn't actually hog all those pins, but rather runs them through itself so that other devices can access them? If this is the case, I guess I should just look up a good diagram of the unit and see what pins it actually uses. Thanks for the help, I will look at the breadboard as soon as I can.

We had the input shield more or less on top of the XBee shield.

That sounds like being a little bit pregnant. It's either on top or is isn't. Since mounting something on top of a shield that only covers half the Arduino is not possible, I'll assume that you mean you don't know.

It's actually all on a breadboard right now.

What is? You've got an Arduino and two shields that both need to be on top - one by design and antenna placement and the other because the joystick is of no use hiding under another shield. So, what's on the breadboard? A loaf of bread?

Unfortunately, I cannot see that breadboard until Tuesday.

But, you're busy writing code. Perfectly understandable. Not.

If this is the case, I guess I should just look up a good diagram of the unit and see what pins it actually uses.

If you know how to read a schematic, why didn't you just do that in the first place?