song wrote
For example, when creating the Mux in Chapter 1, I used the And chip, but it looks like it's not using the one I implemented, and instead it's using a built-in version.
I'm about to start Chapter 2, but it feels like the files I wrote in Chapter 1 aren't being used.
If all the tests have passed, then I guess it's not a big issue—but still, I wish the files I wrote were actually being used.
That is correct. The authors very intentionally made it so that each chapter's projects were independent of the other chapters, as much as possible. This allows students to do them in almost any order. If you want to skip the combinatorial logic and jump straight into sequential logic, the you can just start with Chapter 3. Similarly, if you want to focus on the top-level architecture without dealing with the weeds, just start with Chapter 5 (or perhaps Chapter 4).
If you WANT to force the simulator to use your implementations from prior chapters, just copy over the HDL files from those chapters into the current chapter -- but be prepared for a huge performance penalty in the simulator.
This is also why Chapter 3 is partitioned into two parts, because simulating the larger memory chips all the way down to the DFF level makes them glacially slow in the simulator.