Check out their documentation for how that all works. Depending on which one you use, there will be prompts or features that help you work with mod conflicts and load priorities. FO4 has some build-in mod support OOTB, but there are a lot of tools out there on the internets that make modding much easier, especially if you want to run a heavily modded game. First off, you will probably want to use a separate mod organizer program of some kind.