It really depends on what you want to do. If you want to alter the main campaign in any way, like adding new weapon types, ships or even new or revised missions, then yeah... editing the extracted files in the Nexus folder is the only way to do that. Debugging that will be a pain, however, as Nexus will usually just crash without descriptive error messages when encountering any kind of error and you don't have a Debug console available in the game. The provided mission editor is waaaay more helpful in that regard, but you can't play the campaign or the campaign missions inside of it... not without much additional work, at least.
If you want to create your own single missions or a multiplayer mod, then you don't need to overwrite anything - just create a new mod in the "mods"-folder of your Nexus installation and start modding. Create new systems, missions and/or copy over the default tacticstypes.ini and make your changes to that, etc. - that's perfectly possible and that's what the game also officially supports, modding-wise. The game wasn't really built for campaign-level modding... although it IS possible - just not that easy and not covered by the modding docs available.
