After I install a game,can I delete the files in the GOG Downloads?(After I copy the files to disk). Will that effect the game? What happens when the game needs a patch,such as the up coming one for Witcher 2.

That's a good question. Previously it wouldn't make any difference because of how the patching system works. If they release a new patch you'd have to download the entire file again. I'm not sure if that's still the case with the new downloader, I suspect that it is.

With TW2, those patches are going to be provided through the launcher app, but eventually there will be a unified version including the last patch for download. But that's quite a ways away.

Hopefully that is of some help.