Basically, you file the top of the bridge saddle so the center slants towards the heel and each outside end slants toward the neck. Obviously, you need enough extra height in the action to do this because typically the stock saddle has its high-point near the middle so when you file the top at an angle the string height is going to be lowered some. Both of my KoAlohas and my Kala really needed to be lowered anyway so this wasn't a problem. In the case of my Mainland, the action was perfect so I picked up an extra saddle when I was at UWC this past weekend so I can compensate it.
In your case, if the inside strings are spot on then you're going to want the strings to break over the saddle at about the same point that they currently do, but since you will be filing the outside edges and lowering the strings you'll still need to file the center section to keep the strings at the same height.
BTW, You can pull about ten cents correction by filing the saddle top at an angle. It's not enough to get perfect intonation, but will get you closer. Also, you'll be able to get more correction on a shorter scale than on a longer (assuming that the bride saddles are the same thickness).
You can get more correction with changing string gages. Going from a CM gage string to a CL gage string (A string) on one uke changed intonation by about 30 cents.
John