So I recently downloaded Cyjon’s semester changes mod but haven’t had a chance to play yet. Am wondering should I still do my 2 day rotation where I finish at midnight or change it up to when the seasons change?

You can still play the same rotational time, you'll just be spending less time overall with that sim being at college. Personally once I got this mod I changed my roation to changing households after a semester finished since it goes faster.

I also have CJ's semester changes and I play on a seasonal rotation, but for my college neighborhoods I combine what Miann36 does with the semester rotations. I'll still play the entire uni subhood for an entire season total, but I do something like this:

Spring Rotation
1. Play all uni households for 2.5 days (approx 1 semester/1 year with CJ's mod)
2. Play all main hood households for 5 days (1 season)
3. Return to uni households and play out the remaining 2.5 days in the season until all households are in summer
4. Play all downtown/shopping district subhood households for 5 days

Usually this results in college students graduating halfway through a seasonal rotation. I let them play out their "x hours until sim must leave campus" until the end of the season and then have them move back to the main neighborhood. YA who have graduated but are still living on campus until the end of a season are allowed to get jobs using the job seeking notice board.

I find playing this way (half of uni + normal hood + other half of uni) helps to make rotational play more interesting by breaking up the time spent in the college subhood. I enjoy playing sims in university, but it can become a slog even with the semester changes mod. Doing half and half keeps me engaged and less likely to get bored with the students.