Not sure if you are on Madden 25 or 15...but on M25, The depth charts are screwy no matter what unless you set them all yourself. Thats why alot of people do 32 team chises....to make sure the depth charts are correct. Might be fixed in 2015, but doubtful.
Autopiloted teams will do pretty much everything....it resigns impending free agents, drafts, advance the week, relocate, trade, sign FAs during the FA period, etc... Im not sure if will will sign OUTSIDE free agents during the season, though. For example, if one of your players gets injured and put on IR, I am not sure if they will sign anyone to replace them. I dont recall the CPU signing anyone in mine....although injuries were set low in mine so most eams didnt need to.