Here's what runs in the new engine: Games, rankings, practice, and recruit generation. Everything else still runs under the old, including things like awards, inbox messages, scheduling, recruit action processing, job processing, season rollover, draft. It generally won't take more than 30 minutes to an hour to run both, so normally everything will show up between 2 and 3 ET during game cycles. For non-game cycles, things will happen very close to the top of the hour.
It's not possible to run parts of one engine and then parts of the other. The have to run in their entirety, either old then new or new then old. Since there are things in the old engine that are triggered by the completion of games, I am running the new engine first. So things like recruiting responses may show up 30-40 minutes later than normal during game cycles. I know that will be an adjustment, but it's the best that can be done right now.