I just started out here, and am following the guides for NPC dialogue. But there's no 'new' option in the list of topics when adding new topics in the quest section, it just brings up topics already used by other NPCs in game. Am I overwriting these files by selecting them and reworking them into my new NPC?

Right-click in the list of topics on the left to get the option "Add Topic", and then right-click in the list of topics in the new window that appears titled "Select Topic" to get the option "New." It'll add a new item and you'll be able to name it. Click OK and then you can select and edit your new topic in the quest editor. Note: on my PC after you give the topic a name and hit enter the Geck will seem to freeze and the quest and topic windows close. They didn't actually close, they went behind the other Geck windows.