The only way to update through the NMM seems to be simply to uninstall the older version and install the newer version. But does doing this cause you to lose any settings from the older version, if there were any? Or is there some specific order to do things in, like install the newer version first, and THEN uninstall the older one?

Also, if you do it this way, does this cause any problems with the save game as long as you haven't loaded the game in between the installations? For example, if there is a mod that edits perks, is there any problem caused by uninstalling the mod and then installing the newer version, or does everything stay the same in the game, and you still have all the same perks with the relevant effects, etc., as if nothing happened?

Thanks.

Usually what i do is do a clean save before i update unless the mod says you dont have to..i really like nmm makes its alot easy to use mods if you new to the elder scrolls.

But doesn't a clean save involve turning off the mod and then loading the game and saving? Wouldn't this mess up certain things, like altered perk trees, if the mod was no longer present?

Some mods update fine with an overwrite, others require one to issue commands to disable it before uninstalling.
Be sure and read the instructions on the mod page.

yeah what Michele said..some mods(build your own house) said to do a clean save but i didnt want to lose everything so im just waiting till i start a new game.

So far the only mod I'm using that shows an update in NMM is Categorized Favorites Menu, and it's working fine even without the update.

The reason I'm asking now is because when I tried to start up Skyrim just now, I got a message saying my version of SKSE was older than the current version of Skyrim, and then I noticed that Skyrim was in the process of updating itself on Steam. So if it's the new 1.8 update, I'm expecting that there will be a flood of new mod updates in the next few days. Hopefully everything will just work between now and then.

There is no one size fits all answer to this, follow the instructions of each individual mod author. If they don't have instructions included or posted ask them. Generally speaking every time you upgrade a mod there is a chance for things to go wrong in your savegame, so its best to be cautious. Even seemingly trivial actions like changing the load order of a mod can affect your savegames in strange ways, its best to get these things right before you save. Best to keep things as stable as possible.

Most importantly don't overthink it and have fun

Well, it seems I can't play at all right now because I get a message saying my version of Skyrim is newer than my version of SKSE supports, and then it just closes.

You will need to update to version 1.06.03 of SKSE

Whew, updated to the beta, and all is right with the world (of Skyrim)!

Me to