Here is an interesting articles on guitar setup and maintenance.

The 12-Step Guide to Electric and Acoustic Guitar Setup by The Pick Really more of a maintenance guide but does show some adjustments. Mind you they do nothing for setting intonation on acoustic guitars.

This one does a better job of adjusting intonation on an acoustic guitar

Lastly a discussion with a tech at Long and McQuade Kanata has indicated intonation on acoustic guitar is more commonly affected by the wood around the saddle giving way – so if you see a bow in the top of your guitar or the saddle is lifting then it would affect intonation. Now you can check this with a piece of paper. Check if you can slip the paper under the saddle. If you can it may be coming loose. That said my best sounding guitar which has minimal intonation problems (less than any of my other guitars) I can slip paper under the saddle, so not sure what to make of that.