I was using Climates of Skyrim and everything was fine. However, I decided that the hardcoe dungeons was too dark and so was the night sky setting I chose so I reinstalled the mod and changed those settings. then I noticed it was different in the load order, and my original bash patch was above it. When I went to load Skyrim it said some save settings may be affected so I quit.

1) How do I change the settings I want properly, or set things back the way they were if I can't?

2) How do I make a new bash patch in NMM?

3) Where should Climates of Skyrim be in the load order? Will NMM do that automatically? If so, how?

If you run BOSS it will re-order your load order. You have to use Wrye Bash to make or update your bash patch. Your game should run fine as the climates of tamriel esp's are single files so just replacing them shouldn't effect anything incorrectly in your save.

Thanks. After I use BOSS, how do I update my bash patch in Wrye Bash?

Right clicking the bashed patch and click rebuild bashed patch.

This has to be done everytime you install/uninstall mods. Run BOSS and then rebuild Bashed Patch.

Thanks.

Another thing, i went to the nexus BOSS page and there isn't anything there to download. Where do I get it from?

Look on the mirror page, there is a link.