I'm not sure how you'd set up whatever software would have come with the FastTrack (I use a POD Studio Pro UX1), but once have your processed signal, it should be assigned to sends. Usually it's sends 1 and 2. Figure that out from the manual or something.
Pop open FL Studio, hit Options -> Audio settings, and select your FastTrack from the drop-down menu at the top.
I record using Edison. You'll want to set a mixer track's input to "Send 1 - Send 2", and open Edison as an effect on that channel. Bring up the Edison window, hit record, play, stop recording when you're done. Then just click and hold the Drag button and bring it into FL Studio's playlist; it's the second button from the right.
Usually, I set Edison to record on play, so it snaps to grid correctly, but if your comp's a bit on the weak side, you might not be able to set your buffers low enough to do that. I also usually mute my Recording channel in FL Studio because the phasing from the slight latency screws me up a bit, but isn't noticeable in the final unless I have to boost my buffers to 256 or higher.
Of course, there are other ways to track guitar in FL Studio, like using its built in recorder, but I found Edison to be the quickest, easiest, and most useful option.