Damage?
 

My car suffered a knock on the side as you can see in the photo. Since the knock I noticed today my soft top roof mechanism is making a very unhealthy sound when I operate it.

Could the knock have damaged the mechanism as well?

http://i68.tinypic.com/eukiz5.jpg

Simple: Yes.

What kind of damage I wonder?

And is it a easy fix for the Panel beaters?

Or will someone else have to fix it?

If you look down there you will see the mounting points for all the "shocks" and top rods and some of the points are a ways down kind of behind the panel that is damaged. It is very possible that one is out of adjustment because of a little tweak there. In your owner's manual you will find instructions on how to disconnect the rods so that you can work the top manually in case something snaps, might want to read that in case something goes haywire and you have a bit of an emergency.

Yes, the transmission mounting point is behind that, and that knock may have bent the mounting location. See below video that explains it. You may need to do the same thing to fix it.
https://youtu.be/dyHdXsTNT8o

That is doing to be a very expensive repair if it cannot be done by paintless dent removal. That particular body panel is almost the full length of the car, replacing it will run at least $3k USD. Besides the top transmission I would also check the engine bay fan to make sure it did not get damaged by the side intake getting pushed in.

As Rick described, the rear quarter panels on the Boxster are not bolt-on panels like the front fenders. Instead, the rear quarters are part of the chassis structure and if they need replacement, they have to be cut out and a new panel welded in (along with the requisite grinding, sanding, and finishing). Its a big job and some might say that the integrity of the chassis has been compromised.

Let's hope that a shop can repair without replacement.

How do you remove the dents if you can't remove the panel?

A good PDR (Paintless Dent Removal) guy might be able to work some magic, my guess is that they would try to access the dents by removing the air intake trim and grills, or through the wheel well or engine compartment. It's worth talking to a PDR shop before cutting and welding that body panel.

Your local PDR vendor may be able to get most of the dent out -- but the big benefit of PDR is not having to paint the repair area. Looks like the paint on the quarter panel is compromised already. Is that a reflection or a scuff in the door?

It's a scuff in the door

I took it down to the mechanic for an assessment they said it's gonna need a new quarter panel. I found one at a wreckers in my city for $500 AUD. I have to take the car back to the panel beaters tomorrow. The guy from my insurance company is gonna be there (Assessor) I'll see how much they reckon it's gonna cost.