Heyas

So I am restringing my guitar today because the intonation is way out on a couple of the strings, the top-E string is -37Hz out.. anyway.. I've never been able to get the intonation perfect on this guitar because the saddles don't go back and forward enough. Normally I can get it within 10Hz of perfect intonation. I know that the saddle height also plays a part in this... so I am wondering which way to move the saddle height..

Where should I place the saddle position before moving the height? If the tuning is too sharp (and the saddle position can't move enough to accommodate) do I need to move the height up or down?

I'm really getting sick of having intonation problems.. even after taking it to a store and having a "professional" set it up, I still have these problems. So the only solution I can think of is to learn exactly how to intonate it myself.