Is it an electric or acoustic guitar ?
First is to get a reasonably good microphone. This depends on your budget, and "you get what you pay for" right from a few tens of £ / $ up to hundreds or more.
However there are two main types: Dynamic and Condenser.
Dynamic microphones are generally good for picking up things relatively close by like a voice or an electric guitar amp, but some are good for all-round use.
Condenser mics are generally better at more ambient recordings so if you're recording an acoustic guitar, that might be a better option. A lot of condenser mics use "Phantom power" which is most easily supplied by your mixer. It'd be worth looking into that before choosing which type.
If electric guitar:
You can either mic our amp up for recording (usually best bet as you probably have a sound you like already) OR a lot of effects units have a built-in "Amp simulator" meaning you can plug directly from the effects unit into your DAW - no microphone needed. the Amp Simulator electronically adds the kind of effect you get when you record an amp through a microphone.
Line1 and Pod make such things, and have a good reputation, though other makes have probably nailed it.
I assume reaper and fruityloops can "Multitrack" so if your backing track doesn't exist in them yet, import that first as your first track.
Then by whatever means record your guitar ans an extra track.
You should then be able to play the two together and amend the volume / effects on each so that it sounds how you like it.
Mixing tracks is an artform in itself (best search for topics on that) but if you have "everything but guitar" on one track and your guitar on another, then really you're just amending your guitar volume according to everything else, so should be fairly easy to get a good mix.
To give you a clue of how you're doing, have a listen to a track where you like the guitar part and try to get close to that.
One thing which can catch people by surprise: "Studio tan" .. after a while of mixing you may find you've been listening to it so intensely that you've lost sight of what's good. If this happens, take a break.
Have a cuppa, etc :-)