You have to cut the Mods folder and place it on your desktop until after the installation when you can put it back. Some mods might not work and NRAAS definitely doesn't wok for me. I know Twallan is working on updating it now so he should have a new version out soon.
You should never install an EP with your mods folder in place, just cut and paste it out to the desktop, easy enough.
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You should never install an EP with your mods folder in place, just cut and paste it out to the desktop, easy enough.
Yes, you should delete them and if and when a new version of the mod is available install them then.