Your question is placed on-hold, not locked. It's an important distinction, because it means that you can still edit your question to clarify what you mean and focus your question down to the core issue that you want to solve, and it may get reopened.
We don't really do "under the hood" looks at gamer-specific software like Launchers or Mod managers, so questions on "how" something works aren't really allowed here. Which is probably why your question was initially closed based on the title of your question.
However, I can see in your question body that you've asked a few separate distinct questions:
- Does Nexus Mod Manager overwrite game files?
- Where does NMM put mod files?
- How are mods that contain scripts handled?
- Do I have to launch the game via NMM?
I wouldn't consider questions 1, 2 or 4 'under the hood' questions, at least from my experience with modding Fallout 3 using FOMM (an older version of NMM). Most people who have fiddled with the Bethesda-game mod managers before should be able to answer these.
Question 3 on the other hand: not many gamers are going to know how scripts are handled and this isn't knowledge they would pick up from using the application itself.
I also think that the answers may vary from game to game, so specifically stating which game (or games) that you're asking about would help.
So here's what I propose you should do:
- Explicitly state the game(s) you're asking about.
- Edit your question to focus on Questions 1 and 2 above.
- Remove question 3 entirely.
- Have question 4 as an addendum (it's a simple yes/no and I don't think it needs to stand on its own).
Does Nexus Mod Manager overwrite base game files?
The Nexus Mod Manager is a free and open source piece of software that allows you to download, install, update and manage your files through an easy to use interface. It integrates with the Nexus sites [nexusmods.com]
I'm looking at modding [Skyrim], and I'm wondering where NMM places the mod files? Does it overwrite the original game files when replacing stuff like textures?
Also, do I have to launch [Skyrim] via NMM or can I launch it normally?
I believe something like this would be answerable by us.