I think it’s wise to setup you project as the majority of your material is. So in your case that’s anamorphic.
So there are two things you can do. You can put all your 4:3 material into compressor and adjust everything into anamorphic. You can either crop this material or you can have bars on either side of the screen.
But you can also just put it in fcp and render everytime you make a change in the 4:3 material.
Depending on the amount of footage the choice yours. That means if it’s a serious project and you have to make a lot of adjustments i would go for the first option.