How would I replace specific blocks on structure gen?

I'm making several structures that are very water-heavy, literally just lakes and such. Because of this if I were to break any blocks in order to tell MCreator to replace Structure Blocks and Air, it wouldn't work due to the water immediately filling up the empty air space and making source blocks. I was thinking that I could possibly replace the desired empty spaces with structure blocks to prevent spillage but I'm not sure if that would work. Any tips?