Do a render and see what it looks like.  It's possible that what you think you are seeing isn't the end result.

Also, it's a good idea to get in the habit of conforming or parenting right after applying an item, this way you don't forget.  It doesn't matter if you do it before or after applying a texture, but sometimes a texture will change the appearance of the item and if it makes it transparent you can't see if there is poke throughs or adjusting needed unless you change the transparency in the material room.  So I prefer to parent or conform right after applying the item.

As for rearranging you files, that's ok to do.  Just don't rearrange your geometry or texture folders, or any geometry files you might find installed in the character folder.  But other than that you can sort you files within the '"Library" folder anyway you like.

"It is good to see ourselves as others see us. Try as we may, we are never
able to know ourselves fully as we are, especially the evil side of us.
This we can do only if we are not angry with our critics but will take in good
heart whatever they might have to say." - Ghandi