After the 1st half (which sims at 2:30 AM eastern time) you have 12 hours to adjust your game plan and depth chart. You do this the exact same way you adjust it between games.
Go to the "Office" page, and there is a button on the right for "Depth Chart". There are 2 types of depth charts: basic and advanced. The advanced charts are the only ones that actually directly affect who is on the field. So if you want to make depth chart adjustments between games or at halftime, you must change the advanced depth charts.
To adjust your game plan, go to the "Game Plan" button on the right side of the "Office" screen. You can make these adjustments between games or at halftime.
All of this info should be in the FAQ (or help page...I cant remember what it's called now) and also within this GD 101 thread. I know it's very long, but investing in an hour or so to read over it will answer these and 100's of other questions you haven't even thought of yet.