I am tuned in drop C. When I put the lock on the nut for the two lowest strings (C and G) it makes it so when I tune the lowest string to C while its open, all the frets from 1-5 are off.

If I leave the lock off theres no problem, but I want the lock on so it doesnt go all out of tune and stuff.

Is there a good online guide to intunation, or is this another problem?
If following the instructions on the webpage suggested here above doesn't fix it, your problem may well be caused by downtuning to open C. Alternative tunings generally need alternative setups to get the intonation right. Don't hestitate to turn to this forum again if the problem cannot be corrected by turning the fine tuners at the bridge.