I guess I am fairly new to this only being a member of this site for less then a year and have come up with some marginal teams (as you can see below, a list of my active teams, too many at once?).   Anyways my question is geared toward managing a team.  Once I draft a team I do a few things before and during the seasons.  1.  Set the batting order.  2.  Set their steal settings  3.  Set my rotation, bullpen.  4.  Set the pitch count for my pitchers.  5.  If in a OL, i'll release all my 200k guys and wait to see if i need to pick anyone up off the waiver wire.  6.  Normal line up/rotation/bull pen adjustments (rest players when needed)  So they are the 6 main things i do...my question is what other things am I missing that could improve my teams?

Current Teams

Wave Patrol X  94-69

Wave Patrol XI  64-50

Wave Patrol XII  82-47

Wave Patrol XIII  60-51

Wave Patrol XIX  67-59

Wave Patrol XVII  71-61

Wave Patrol XVIII  85-50

Wave Patrol XXI  69-48

Wave Patrol XXII  67-53

Wave Patrol XXIV  73-47

Wave Patrol XXV  16-20

Wave Patrol XXVI  11-7

Wave Patrol XXVII  13-5

Manage fewer teams so you can study each one better.

Building a team is at least 80% of the battle... There is only so much you can do (short of a couple of extreme strategies) to improve performance with managerial settings. 

I did notice you didn't mention in-game rest settings, player higherarchies and PH settings.

Boog is correct.  If you have too many teams, unless you're one of those rocket scientist like Boog, you won't be able to devote the time and attention to each of them as they may need. I found this out the hard way when I had 12 teams going at once.  I would forget to set them, and then 10 mins before the games are about to sim, I found myself rushing to set them and made many mistakes, like leaving 2 or 3 starters in AAA at the deadline (twice), forgetting to reset my SPs PC after having set him to 40/40 his previous start for some rest, etc.

To be honest I don't get/understand the in-game rest settings.  

The in-game rest settings are a two part function.  First, the setting you have on the rest portion of the "Team Managerial Style" will dictate whether or not rest is used.  If you uncheck the boxes for "Rest players if winning/losing by X or more runs in the X inning or later", then no players will ever rest.  If you do check this option, then it will allow for players to automatically be rested if winning/losing by whatever margin you set.

The other in-game rest setting are the "autorest" settings found in the "Advanced Settings" area, and involve the "Allow Rest" checkbox (check for yes, uncheck for no) and the percentage next to their name.  If you do allow rest, and the player/pitcher is below this number prior to the game starting, then Sparky will automatically rest them until they recover above this number.

All position player rest settings can be set in the "Player Hierarchies" popup.  The thing to know about this is that at each position, the player you have listed to the furthest left will be the first player Sparky checks to see if available for rest.  If you put your starter furthest left, they will not be taken out of the game for resting purposes even if your backups are listed next.  You must order each position left to right by which player you would want to come into the game first for resting.

Hope it helps...