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You'll have three options.
1. Work in a 16:9 sequence and show black bars on the sides of the 4:3 stuff.
2. Work in a 4:3 sequence and letterbox the 16:9 stuff.
3. Work in a 4:3 sequence and crop the sides of the 16:9 stuff so it fills the frame.
1. Do you have to create the black bars on the sides for the 4:3 stuff or does it do it automatically? I do not have any 4:3 footage to play with, this is for an upcoming project I'm planning for.
2. If you import the 16:9 footage into a 4:3 sequence isn't it automatically cropped with anything extending outside of the 4:3 not displaying?
For # 2, if you have Scale to Default Frame Size ON, it will, but if you do not (and many chose this method for more control), you can then use the Fixed Effects>Motion>Scale, and Motion>Position to get exactly what you want.