PC---> Micro Controller ---> Devices HELP

hey,

I am in the process of building an underwater ROV. The ROV will be driven by two joysticks which will connect to a computer. Attached to the computer will be circuit 1 and attached to ciruit 1 will be circuit 2. Within ciruit 2 is sensory devices and motors that will be controlled by the joysticks. The electronic components will look something like this...........

HOOKED UP TO COMPUTER (circuit 1)
**broken link removed**

HOOKED TO ABOVE CIRCUIT VIA A CAT-5 CABLE (ciruict 2)
**broken link removed**

Building these circuits is no big deal as i have built many before but I am wondering how the Atmel mega32 will work with the computer because i know nothing about micro controllers.

Do I have to program the micro controller so that all of the devices will send info back to the computer and vis-versa with the joysticks.
Or will a computer program be able to control the micro controller without us having to do any programing on it.

I will be using the 40-pin PDIP
http://www.avrfreaks.net/index.php?module=Freaks Devices&func=displayDev&objectid=69



If anybody has any answers or good tutorials on this it would be much appreciated

Ben

the microcontroller is just a small computer. you will have to write code for all the tasks.