I recently purchased a honda 400ex, it is the first sport/performance quad I have ever purchased. I'm trying to familiarize myself with its components. I was hoping to get some input on the prolink suspension which it comes equiped with. I'd like to know any websites which would explain how it works..or perhaps anyone with knowledge in this area could explain it to me. Thanks.

It has to do with the linkage at the bottom of the rear shock.

The rear shock, instead of being directly connected to the swingarm, is connected by linkage that attaches to the frame on the front side and the rear of the swingarm on the rear.

This allows them to make the rear suspension's action more progressive. On the 400EX the shock moves pretty slowly through the first 2/3's or so of it's travel (compared to swingarm movement), then the last 1/3 or so the shock compresses more per unit of swingarm movement. This all means that the swingarm has less leverage against the shock the farther it is compressed, basically making the suspension "more stiff" the closer it gets to the end of it's range of motion.

so if i were to get a new swing arm, i would still be able to use the prolink design? or do i connect it directly to the swingarm?

I believe most aftermarket swingarms utilize the factory linkage, but there are some that directly connect the shock to the swingarm, talk to the manufacturer before ordering to find out which is right for you.