The bellhousings are interchangeable to the motors. Any 1937-1959 216, 235, or 261 chevy bellhousing will bolt up to any 1937-1959 chevy motor. The same is true with gmc motors and bellhousings from 1939-1959. In fact, the gmc bellhousings are interchangeable with the chevy bellhousings.
The trick is to use the bellhousing that fits your chasis the best. In your case it will probably be the 1937-1946 bellhousing on the 1955 motor. This will allow you to run the stock transmission and torque tube behind the newer engine.
If you want to change transmissions you have a few options.
1. Use an adapter plate between the bellhousing and transmission. This works extremely well when putting a T5 behind a stovebolt with the early 1937-1946 bellhousing.
2. Get a modified 1947-1954 bellhousing. Ok, it might actually be 1948 or 1949 and later to have the correct bolt pattern for a muncie or saginaw 4 speed. The 1947-1954 bellhousings will bolt into a 1946 frame with the 1946 rear motor mounts and crossmember. These bellhousings will not bolt to the clutch and brake pedals... unless they are modified.
3. There are many other options but they all require more fabrication.