Changing the strings on your 12-string guitar can be a real hassle. Try this, it will take half an hour or so:

Loosen and remove the low E (sixth) string and it's accompanying higher octave string. Using a soft cloth (and optional guitar-cleaning agent), polish the exposed portion of fretboard and headstock. Restring both strings, taking care to keep the higher octave string in the top (closest to you) position.

Bring each string approximately 1-1/2 inches past it's appropriate tuning peg. Make a 90 degree angle bend in the string at this point. Feed the string through the tuning peg, up to the bent point. Bend the string at the point it protrudes from the tuning peg. This will hold the string in place as you tune it.

Bring the strings into approximate tune. Since pitch will change somewhat as other strings are being changed, exact tuning is not required at this point. Using a pair of pliers, cut off the excess string, leaving approximately 1/4 of an inch of the string protruding from the tuning peg. Repeat for each of the remaining five string groups.

Using a tuner, fine tune the pitch of each string. Standard tuning for the 12-string guitar is as follows: E(upper octave),E | A(u.o.),A | D(u.o.),D | G(u.o.),G | B(unison),B | E(unison),E

Tips:
Optionally, to relieve neck tension, a 12-string guitar can be tuned down a tone (D,D,G,G,C,C,F,F,A,A,D,D) and capo'd at the second fret.

From: http://guitar.about.com/