How flexible is tying content to a structure?
Structures simply add an extra bit of sorting and querying. You can look for entries in a structure the same way you look for entries in a channel. The difference is that you can also have parents and children in a structure with a manually set order.

If you look at the section page for a structure and hover over an entry, you will see a move handle. You can use that to resort your entries in any order you wish. You can also move the entries to become the child of any other entry. Taking three child entries of a top-level nav and moving them to another top-level nav is no problem.

How you organize your content is highly contextual. I don't know what kind of site you're building, so I can't say what's best for you. Most sites I've built thus far have only needed channels save for one. And for that one, I have two structures and two channels. I'm using one channel for news entries, and the other for event entries. I'm using a structure for static pages so I can sort them into a hierarchy (and it gives me breadcrumbs). I'm also using a structure for the main menu because it needs to be set up somewhat different than the static pages (and I need extra fields). This was all chosen based on the needs of my client's site. So just think about your client's needs. Will they be editing it? Is how you have it set up now easy for them to understand how to edit?