What do you mean, manual install? There's no such thing, as far as I know... considering that there's a bunch of files spread around the cds, that are probably compressed and you need the setup tool to decompress. Why exactly can't you use the normal setup?
The game starts to install but the progress bar does not move at all, then after 5 mins it just dumps me out to desktop with no error message. I had the same problem with doom 3 but managed to find a guide on the net to manually install it by copying all the pak files of all CD's into a base folder.