How do you record a guitar cover over the orginal track with a M-audio interface?

I have a M-audio mobile pre and was wondering how people record guitar covers but have the track playing on top of the guitar they are recording? Also would i get a better sound just directly using my guitar plugged into the M-audio unit with like an amp plug-in on FL studio or using my actual guitar head and my celestion speakers using a shure sm57?
ESP LTD EC-1000 vintage black
sunburst fender MIM tele
Epiphone LP standard ebony
Mesa/boogie dual rectifier
Mesa/Boogie .50 caliber plus head
Marshall JCM900 Hi-gain MII 2500
Fender Hot rod Deluxe
Im not sure about how to import the actual track onto your recording. I know somr programs have a way to rip it form the cd and put it as a track on the program but i dont know the process of it. As for the sound quality, I would try both with your setup and witht eh plug-ins, but I think you'll be happier with the sound of running your amps and stuff into it as opposed to the plug-ins.
When all else fails.......Shred!!
Do you record in FL Studio? If so, I would advise against that. FL Studio is mostly a sequencer, geared more towards hip-hop and electronic music. DAWs like Pro Tools, Cubase, Reaper and other can record, edit, sequence, and other things.

Like Metalhead said, your DAW will be able to import audio, so if you have the .wav or .mp3 file on your computer, you can import that into your session. After that, just create a new audio track, and record your guitar.

As for amp sims vs. miced amps, it depends. Typically, (good) amp sims are easier to use and you can easily dial in a pretty decent tone. However, it's hard to beat a great-sounding, well-miced amp. That being said, you'll have to spend some time finding just the right place for the mic. A 57 will work just fine.
^ FL Studio has changed a lot over the years, and these days it is much more than a sequencer. i wouldnt say it is particularly worse than any other DAW you mentioned for recording.