Day parade starts in Frontierland and ends on Main Street. Spectro Magic starts on Main Street and ends in Frontierland (even if there are 2 scheduled...they will both start in the same location)
Here is the train run down... I hope you can follow this, I have worked on the trains for 5 years so it makes sense to me but it can be confusing.
Parades:
The train will "HOLD" for the parade it will not stop running. For the normal day parade it will hold for about 6 or 7 minutes while the parade floats cross the tracks in Frontierland. If you will be there for the Christmas Parade the Trains will shut down for about 45 minutes to an hour because that parade is so long when the first float is getting to Main Street the last float is just leaving Frontierland. For the day parade the train can not cross through between floats...
For Spectro Magic (see Fireworks scenario below as it may affect this)... They have built in crossings (holds between floats) where the train can get by in Spectro Magic. So they do not change the operation for Spectro.
Fireworks:
This is where it gets tricky. If the Fireworks are AT park closing time the last load for the train will leave Main Street 1 hour prior to fireworks. So if the fireworks are at 9pm and the park closes at 9pm, the last pick up will be at Main Street at 8pm. The train will then go to Frontierland and pick up, Toon Town and pick up, Back to Main Street to drop off (no more pick ups), Frontierland to drop off and back to Toon Town for the final drop off, where it will then back off onto the spur line and head back to the round house.
If the Fireworks are not at Park closing time (say there is a parade at 9pm, Fireworks at 10pm and a second parade at 11pm with the parking closing at 11pm) The Train #1 will pick up at Main Street at 9:20pm and do one full loop around back to Main Street. It will then hold at Main Street through the fireworks and resume service once the fire marshall has checked the tracks in the fall out area to make sure it is safe. Train #2 will pick up at Main Street at 9:30pm and will only go as far as Toon Town where it will unload everyone and sit through the fireworks and wait for clearance to resume. Once they are cleared to resume they will continue service until the park closing time. The Last train for the night would then leave Main Street at park closing (11pm in this scenario) and do one last trip around picking up at all the stations. When it returns to Main Street everyone will be asked to disembark and the train will leave Main Street empty to head back to the roundhouse.
I really hope that that helped to answer your question and did not confuse you more.