Open up a Shell or CLI window, type
Ed S:/Startup-Sequence to open up the built-in text editor, cursor up to the first line, press Enter a couple times to give yourself some space, enter the ACAtune commands, then press Esc+X to save. Make sure you don't edit anything else if you're unfamiliar with Startup-Sequence commands!
The options you pick will be specific to your card, as paul1981 said. This might help:
http://wiki.icomp.de/wiki/ACAtuneAlthough I'm sure if you post what model card you have, someone will come along and tell you the best string of commands to use.
