You play this game like this:
1. Make all side quest that open up, your main priority e.g. Sandra & Pam quest-line/individual story opens up.
2. When above happens, STOP Main quest and School Quest. Play until Sandra and Pam quest finishes. Doesn't matter the order of side quest, you can choose to finish Pam before Sandra and vice-versa.
3. When all side quest / individual stories that opens are completed. Then and only then you may continue with Main quest and School quest.
NOTE: Some and only a very few, side quest / individual story would require you to go back and forth with Main or School quest. Do this only when the game tells you to, i.e. BOF (Book of Faces)
Now for the teleportation, if you teleporting during on-going quest, this can cause issues in your save and break your missions. But I doubt you doing this cause it is obvious not to teleport during a quest

.
Basically when on
mission/ongoing quest, you only teleport when the PLACES ARE LOCATIONS YOU
CAN RETURN TO & NEVER WHEN INDOORS
On the other hand, when
NOT on mission/ongoing quest, teleportation is fine anywhere (including indoors)
Hope this helps brother