I'm decided to go about installing my mods using Wrye Bash for this play through as I like how it handles mod conflicts in particular. My question, on a related note, is how do you deal with conflicts on mods that don't have a .esm or .esp? For example, using the Skyrim HD texture mods as well as things with similar files that also don't have a .esm or .esp like Rain's Clutter Improvement. Also, am I right to assume that anything with an active mod component such as SMIM will be automatically be prioritized over Skyrim HD? All in all, what do I do to sort out the conflicts in these situations?

Sorry if this is an idiotic question, but I just can't seem to figure it out.

Thanks.

It all depends on install order, with or without Wrye Bash. The one installed last is the one that shows ingame.

Difference is that Wrye Bash will show the conflicting files, and allows you to change the install order easily.

So to change the install order, am I just uninstalling all the things that conflict with them and then re-install them in the order I would like?

That's the long way to do it. Or, you can just click and drag the files into the order you want within the Bash Window. BOSS can also do this for you. Although BOSS wants and ESP or ESM to apply the order to. BASH would be better for textures only.

Just drag and drop in the installers tab? If so, you just made my life a hell of a lot easier. Thanks you two.

TES Alliance have a useful tutorial here: http://tesalliance.org/forums/index.php?/tutorials/article/120-getting-started-with-bain-installers/