There is plentiful lodging near Old Town Sacramento where the museum is located. There is a Ramada across the river, and if you want something different, the Delta King riverboat tied up in Old Town is a hotel. I've never stayed there, but I heard it was nice, if somewhat noisy at night. Stop in at the California State Railroad Library adjacent to the museum. Well worth a visit.
Keddie wye is easily accessible with a nice overlook on State Route 70. SR70 ( Feather River Canyon hiway) follows the old WP main all the way from Oroville to Portola with many beautiful photo spots. The only problem is, there are very few trains on this line these days. The UP uses the Feather River route only for westbound manifests and loaded grain trains. This can be as few as 3 trains in 24 hours, but 4 or 5 is probably average. (two North Platte-Roseville manifests and a couple of westbound grainers.) There are at least 2 BNSF trains west of Keddie each day so you should have at least 8, or 9 trains up the canyon, but still not that many. The BNSF trains go up the Inside Gateway to Klamath Falls, so through Portola is very quiet at times. My last trip down the canyon a couple of years ago I did not see a single train, the first time that's happened in a couple of dozen trips up the canyon.
The Western Pacific Museum in Portola is well worth visiting. In my opinion the best individual railroad themed museum in North America. Spend the night at the Pullman House B&B with a room overlooking the east end of the Portola Yard. You can see trains being recrewed and know you will have something moving shortly.
Roseville yard and the newly built retro station is a good place to watch trains. This is at the east end of the yard where line over Donner summit and the Shasta lines diverge. Fairly active with yard jobs thrown in to the mix. Donner Summit and Lake is really beautiful with far more trains than the canyon. Perhaps one way up and the other back. Use SR89 between Truckee and Portola. It is a good fast road, although not particularly scene. Avoid SR49, which is very scenic, but also very windy and slow (with no trains). This part of California is so scenic that you can hardly go wrong on a visit, even if you don't see many trains.