I run BOSS to set my Load Order.
I use BAIN to install mods, and I adjust my Installation Order (in Skyrim) to match my Load Order.
If a mod has a readme file, use it to find where the mod should go in your Load Order.
You can manually adjust a Load Order with the default Skyrim Launcher, but BOSS is faster.
If BOSS does not recognise where a mod should be placed, then look at what the mod adds to the game, and place it next to other mods that are similiar.
This is a sample Load Order,
Skyrim.esm
Update.esm
High Res Pack 01.esp
Hgh Res Pack 02.esp
Unofficial Skyrim Patch.esp
Noises.esp
Tweaks.esp
Weapons.esp
Clothes.esp
Armor.esp
House.esp
City.esp
Quest.esp
Companion.esp
Hope this helps a little, and use the links in my Signature.