Here is a link to Twallan's "Which Mod FAQ"
https://nraas.wikispaces.com/Which+Mod+FAQYou might find it helpful and I'm sure it's been posted before.
I know the moving of folders can be annoying, but you should only have to do that when a new patch is released. If you're going to use mods, I'd recommend turning off the Automatic Updates so you can decide when you want to update. I know a lot of people won't update their game until Twallan has been able to update his mods. The good news is he's very dedicated and fast.
Also, there is a matter of maintenance on mods. Like anything else in software, they require updating even between patches. When problems are found, Twallan is good about fixing them and updating the mods. He has a special page for Update History:
https://nraas.wikispaces.com/Update+History And there are instructions there on how to get e-mail notifications of updates. I'd recommend that so you know when you need to get the latest version.
For me, the general maintenance is very worth the outcome because I enjoy the game so much more with his mods that I use.
Regarding Story Progression: If you get Story Progression, you'll need to also get a module for Master Controller called Progression. You'll probably also want the module Cheats.
More tips: I have a folder on my desktop where I keep the zip files from NRaas. The zip files shows the version. However, the package file that is installed in your mods folder does not. So it can be hard to remember which version you have. So I have that separate folder to make it easier for myself. When I get a new version, I simply install it from that folder and then remove the previous version.
When a new patch is released, you'll need to have some patience for the mods to be updated. You can either remove the mods and update. Or wait for the mods to be updated and then get the patch. Totally up to the individual.
NRaas has it's own Chatterbox discussion board which is very useful if you have a problem with an NRaas mod and want some friendly advice. Everyone there is very helpful and don't discriminate against those who aren't very computer savvy. I frequent the forums here and NRaas Chatterbox and that's about it.
Lastly, I'd recommend you get the basics in the mods first (Master Controller with Cheats, Overwatch, Errortrap and Saver). Get used to those first before getting into Story Progression.