IR communication for swarm bots

Actually i am an architect, so I'm quite out of place both on the programming and on the elctronics side... XD
I wanted to ask you just one other thing. I cannot really understand how the interrupts really work. Mainly, I will need to drive motors according to the IR signla received, in order to control the movement of each robot in relation to the other robots position. What I cannot understand is if the interrupt stops the code and then starts from the point that it reached, or if it starts again. Also, I wanted to ask you if there is a way to control the interrupt with conditionals, let's say, check the IR reveiver just one time each 2 seconds...
Regarding the Arduino, I'm using an Arduino Duemilanove and an Arduino Uno, so I do not really know what are the performance of the 8Mhz board. What would you use it for?
Thank you again for the help!