Bernina Express - late April

The Bernina Express is the only train that requires a seat reservation. If you overnight along the way, and want to continue on the actual Bernina Express train, you will have to buy two seat reservations. On the other hand, the regular hourly trains that ply the route do not require reservations and they are unnecessary. Just board any train you want and hop on and off the rest of the day along the route shown on the ticket.

Pontresina is the logical place to overnight. If you want to ride the named Bernina Express, the section from Pontresina to Tirano would be the one to ride. Take a regular regional train from Chur to Pontresina the day before; no reservation necessary or even possible.

The Bernina Express is no faster than the regional trains (it can't be, it runs on the same tracks and trains can overtake). It also makes intermediate stops, so you can do part of the route, you don't have to go all the way. The only differences are:
1) It does Chur to Tirano on one train, on regional trains you have to change trains.
2) It has reservations. No reservations possible on the regional trains.

Pontresina is a popular choice for an overnight stop, you could choose anywhere. St Moritz (slight detour), or anywhere in the Engadin valley.
This webpage from the RhB (the rail company that runs the line) has a map with places lsted:https://www.rhb.ch/en/panoramic-trains/bernina-express
The thin red line Tirano-Lugano is a bus connection. The rail line is shown in grey, down the east side of the lake.

Make sure the place you choose on Lake Como is on the east side (for example Varenna), this is the side the rail line from Tirano to Milan runs along. Places on the other side need a ferry across the lake to get to.

Just elaborating Chris F's reply just above - the trains between Tirano and Milano calling at Varenna are on the east side of Lake Como and go via Lecco not the city of Como.

The reason the Bernina Express is no faster than others is that it is single line with short stretches of double track at certain stations. At those stations the first train at a station waits for the train from the other direction to arrive so they can both leave and neither is blocking the other's route. They are timed so that if they go at the normal (very slow) speed they cross with minimal delay to either - so all the trains, named special tourist train or regular normal train, go at the same speed. There is nowhere for a train that would be faster to overtake a slower one, and there are relatively very few special ones.

Do not equate the name "Express" with fast or faster - it isn't.

East / West - oops. I corrected it.

Thanks! Didn't really think it would be faster, guess I was wondering if the amount and choices of stops would be different. From what Ive read, it looks like the regional train is cheaper and potentially less crowded?

The regional train often stops at all stations, and passengers can join or alight. The named train will stop there too, in order to cross with another, but the doors remain locked. Bernina Express only makes actual station calls where passengers can join or alight at a limited number of stations.