I want to use my BotBoard connected to my SSC32 to control my Pheonix via an Ipaq 2200 PDA with a custom program where-as I would send the variables from the PDA to the botboard which would have the stored “movements” and excute them. How would I hook the BlueSmirf up to the BotBoard? In the Lynxmotion Tutorial, It says to hook the leads to the TX and RX pins, but the BotBoard does not have these pins? Where do I hook it up to and will I need some code written for it?
well the bot board when populated with an atom pro type module can define any of its 16 i/o ports as software serial ports (i.e one port for RX and one port for TX). in this case it might be better to use the hardware serial on ports 14/15 (I think that’s right) so you can use the hserial functions. this has the advantage of being interrupt driven and buffered so you don’t have to spend processor time sending bytes or more importantly waiting for them to arrive (asynchronously). 
So, can I still use my wireless PS2 controller as well? Right now, it is using those pins, or would that cause too many conflicts?
It all depends. As you noticed, the hardware serial port uses pins 14 and 15 and currently your PS2 controller is using pins 12-15. So you would have a few choices.
You could put the bluesmirf on other pins and not use the hardware serial port. This works pretty well if you are mainly transmitting from the bluesmirf as doing serin’s from a normal IO pin will only capture the data that was actually transmitted while you are sitting in the serin. There are several ways to make this work, which includes things like you outputing some type of poll message from your BB2 to the PDA that would say I am ready and the PDA has so much time to output the data…
Alternatively you could use the hardware serial port and move the PS2 to another set of pins (not 4-7). The problems here is you will need a pull-up resistor soldered in to the DAT line to make this work.
Not sure if that works for you or no.
Good Luck
Kurt