EQ (Enigmatic Question)
Yes.
Don't.
Unless it's absolutely necessary, that is.
Actually, you need to give more specific information in your question. Generally speaking, always try to get the best sound in the recording stage by experimenting with mic positions first before you reach over to tweak that eq.
For direct, line-in recording, adjust your eq on the guitar itself rather than on your recording device (assuming your acoustic has one of those nifty "hi-lo-mid-presence" preamp thingies on it).
Again, you don't provide enough info for anyone to help you in a more specific way. What kind of music are we talking about here? What else is in the mix - bass/drums/keys/horns/sax/electric guitar/bagpipes/organ/kazoo/???
Run a CD player though your recording system so that you can monitor back and forth between the CD and what you're trying to record. Obviously, it should be a commercial CD of music that is similar in style and orchestration to what you're trying to achieve yourself. Do whatever you have to, eq-wise, to make your thing sound like the commercial thing. Be s-p-a-r-i-n-g on the eq. Only boost or cut enough to make the difference you want or need. Too much fiddling with eq can add extra noise and cause all manner of phasing problems should you get tweak-happy.
Remember, too, that in the end, it all boils down to what sounds good to YOU.
Bruce in Korea