You can use I2C to communicate between PSoC and Pandaboard. you must configure one of them as Master and the other one as Slave. Since in I2C it is the Master which initiates the communication and generates the clock, the device which has to send commands to the other should be made as a Master.
Alternately, you may also consider UART for communication. In this protocol, there is no Master - Slave relation. If used in Full-Duplex mode, any device can send to / receive from other device. Pandaboard has DB-9 connector for RS232.
The principle of I2C is plain and easy to understand: The slave obeys master (Gollum principle )
This means: The master writes into the slave(s) and read from the slave(s). Note the plural, I2C is made to control several slaves. So no method exists for a slave to talk to the master (asking for support, waking-up master etc) initiated by the slave.
On the other hand UART was made originally for communication between man and machine (woman as well) and both may initiate an 1 to 1 conversation. Additions have been made (and implemented in PSoC of course) to talk to several devices on a bus-like structure. The advantage (in my opinion) is, that the "slave" may initiate a conversation (asking for recharge of battery).
I would select UART.
Please also be aware of the limitations on the dat throughput that you might need between PSoC and Pandaboard.
I2C is easy enough to implement on the PSoC.Surprisingly easy,if I might say so.
I have interfaced an I2C EEPROM,and you can check out my blog post on the same.
As far as control of motors is concerned,you could hook up a regular L298D(depending on your motors' current requirement) and control it easily with the PSoC.
Hope this helps :-)
Since you have to establish a communication - path you will have to define something like a "protocol" that defines who and when may talk to which. It would not be unwise to have a brief look at the OSI-modell to see how this fits in your situation/project. Look here http://en.wikipedia.org/wiki/OSI_model . The requirements for the protocol will make it easier for you to decide which interface (or interfacES!) will be the right choice.
I prefer use UART and if you need communicate more boards, use RS485 (not problem with noise environment, no problem with distances, etc,etc). One point to keep in mind it's very easy depurate if no trasnmission exist
I've done a 1/2 CNC with PSoC1 (I'm finishing now with PSoC3), 3 boards (1 a axis), everything with RS485.
Besides I've developed a 32 servo controller (with PSoC3) and communication with RS232. (you can see "el bicho" in youtube Look for hexapod PSoC3. I know the quality is very poor. Sorry )
I prefer I2C over UART since you can connect multiple slaves to 1 master. It's true that slaves can't initiate connection to the master but you can just make the master poll each slave one at a time.