at the moment I have my horses all paired up, but as it comes to breeding time I've been thinking, stick to the partner they are paired with or breed highest pointed mare to highest pointed stallion?

You could do that, but then you might end up with foals with far fewer points than others. That'll only happen if there are serious point differences though, and if there aren't, then you wouldn't make a huge impact on foals' points anyway... It seems easier to just stick with the current pairs. It might even be easier to keep track of lines that way.

Or you could do highest mare with lowest stallion since mares points contribute more? I did that so all the foals had roughly a close amount in the starting pts...

I usually have mine paired up according to how they were named. Like my coyotes are paired up by song.

Link Tree

I usually try to stick to pairs that were already established. That way, I don't risk "inbreeding."

If you're looking for a point boost, I sometimes use the Cash Shop's option for the 1% breeding boost from each parent. 

Hope this helps! :)