I think I got the screen off eBay for around £10. But seriously, I'd take it to a shop/repair centre to do it. If you get more dust past the screen into the viewfinder it's game over and you'll end up with a bill as big as the one I had.
As far as I know, the focus screen us purely for your reference as to where the camera is focusing. When I looked into how it all worked, I seem to remember the focus system, on the 450D at least, is at the bottom of the camera - I think the mirror is semi-reflective and a small mirror behind the large mirror sends light downwards to the metering and focus system. Of course, I have no idea if this is true of all Canon cameras.
If you're still getting focused shots then I'd say it's not having any impact on the workings of the camera. If you can live with the focus screen looking how it does then it's not an urgent thing to replace. I really messed up mine though so had no choice but to do it - every time I took a photo it reminded me of how stupid I'd been!