Hello, well one of my friends Sqiure's neck has snapped, Please don't ask how even i don't know, well he has been playing for not even a year and knows almost nothing about the instument, anyways I helped him replace the neck with some other generic electric guitar which doesn't even have a brand name..

Anyways when the neck was put on and the strings were on and everything, when i tried to tune it, it wouldn't tune properly. I once heard about checking the harmonic on the 12th fret so i checked it to the fretted note and it was a Whole step off. So I was wondering if anyone could tell me how to adjust the intonation, I would take it to a music store but... The nearest one is about 50 miles away... and i don't think this thing is worth the time or money of going that far, so could somebody please help.
make sure that the new neck is the right scale length and if so, in the right position on the guitar. To do this, measure from the nut to the 12th fret and then measure from the 12th fret to the e string. They should be the same length and if not, you should be to make them the same length by adjusting the bridge saddle. If they are too different to be able to get same length via adjusting the saddle, you will need to change where the neck bolts onto the body.

There is a good discussion in a current thread regarding intonation and how to check - I think the thread is called 'First Build - Intonation Problems' or something like that about 4 threads below yours. read what guitarexplorer and mr. flibbe describe (sorry if I missed the other commentors
That does seem a mighty long way off for intonation to be.

I don't mean to sound patronising or anything but...
Does the new neck does have the same number of frets as the old one? And is the scale length the same? Those are important things to match up otherwise you'll never get the intonation right without physically moving the bridge.
Quote by Rusty_Chisel
...measure from the nut to the 12th fret and then measure from the 12th fret to the e string.
I think you meant to say, "...from the 12th fret to the saddle." To the e string is a little vague. Other than that, spot on.