I'm ashamed to say I've never really looked into the auto-rest options until tonight.  So I was wondering if someone could help me understand how it works.

If I have my player rest chart setup, and autorest for each player checked and set at 99%, will the AI change my lineups when players hit 99%?  Are there any other places I need to complete for this?  Does it really work?

Thanks in advance for any and all guidance.

Your basic understanding is correct. You will need to complete the 'rest heirarchy' in the managment menu. Assuming the backup listed in the heirarchy is above his autorest level and is set to 'bench' rather than 'rest', he will appear in any game that the primary player reaches 99% (or whatever you set it to).
Personally I don't use this. I prefer to do it manually that way I can readjust the batting order optimally.

Also, in the same menu that you choose an auto-rest level (Manager's Office > Player Settings > Edit Player Settings) you'll need to make sure that the 'allow rest' box is checked. That box usually is by default, but make sure.

Thanks!  I'm really just looking to reduce the strain of managing my minor league teams, so I'm okay with the batting order being off.

also...you need to make sure that the bench player is listed to play at the position you want him to go in at...I do this for all of my minors...greatly cuts down on management time