Hey there I'm having a major problem with my intonation which is preventing me from playing my guitar. The B string intonation is majorly messed up, when I fret the 12th fret it is flatter than the harmonic and no matter what kind of adjustments I make to the saddle I can't seem to fix it. I would rather learn to fix guitar problems myself instead of going to a guitar shop to have them fix it, but if this is a serious problem which needs professional adjustment then I will have no choice, but any help would be great.

Make sure you have new strings when you sort your intonation out.
What kind of adjustments are you actually doing to the saddle?
You should be moving the saddle forward if it's flat just to make that clear.

Is your FR bridge set up properly to begin with? If it's not level it'll not intonate properly either.
Other things that will affect your intonation is string gauge, action and neck relief (truss rod adjustment...but if your neck is straight, forget about this).
Things with strings:
Ibanez J.Custom, Prestiges, RG8, SR5 bass etc
LP's, Strat, Tele
ENGL Retro Tube 50
5150 III 50W
Orange Terror Bass
Yes--bad strings can affect intonation, but so can an improperly set-up guitar. The best guide out there for setups and intonation was written by Rich Harris. You can read all of the info here:
Oh, frack! But, I didn't say frack--I said "THE" word. The F-dash-dash-dash-dash word.