If the string is flat at 12, the saddle would need to come forward slightly. Intonation can very as much as 30% from string to string, so sometimes swapping a string out can produce better results. Also the string action is a factor, so adjusting the saddle height can affect intonation somewhat as well. Probably the best suggestion is to try a few different things and see what the effects are. You only have a few variables to manipulate, so go for it. Try a different saddle, or slightly raise the action a little, or swap the C string out and see what happens. How flat is the string at 12? If its only a small amount I might just not worry about it.
Depending on how you play, it might be more advantageous to have the intonation more accurate in frets 1-7, so keep that in mind. If you "fix" the 12th fret intonation, you may very well negatively effect the 1-7 action, which is often very noticeable. I play a lot of things higher up on the fretboard, but don't really very often use the 12th fret C (since that note also exists at the 8th fret of the E string). Intonation on ukulele is often a "best case scenario". Its very difficult to have a perfectly intonated neck and usually compromises must be made somewhere. Good intonation is most valuable where you play the most, so be sure to check the lower frets intonation first.
Most people learn to check intonation by tuning the open string and checking the 12th fret for accuracy, but really you should be checking the lower frets first. Ukes are often sharp in the first 3-4 frets, so sometimes the 12th could be intonated flat to counteract this issue somewhat. Anyway, just my 2 cents. Good luck!