Under linux, you'll most likely will need to use manual patches.
is your friend.
Another hint is a patch will COPY then PATCH a file, not patch in place. So if you run sisi, you can just do,
cp -al EVE/ EVEsisi/
and you get hardlinks instead of lengthly copy for sisi. It's a little bit risky that CCP will change their patching behaviour, but "copying" takes 1s instead of minutes :)
I also hear that OpenSUSE is good for you
and supports nvidia drivers.