Here's my list of tips for modding Skyrim:
1) When using LOOT, FNIS and SKSE, run them through MO or they probably won't work properly.
2) Use Mod Organizer. Seriously, the fact that it doesn't actually overwrite anything is a very big deal. NMM is pretty terrible at managing Skyrim mods.
3) Run FNIS any time you mess with animations. Tick the first two boxes and leave the rest unchecked unless you are running the specific mods each one mentions. Flush the animations and update them in the SkyUI MCM, reset in Sexlab.
4) Read the mod instructions. No, really. Read them. You will fuck everything up if you don't.
5) Do not use script-heavy mods. If the description mentions being script-heavy, just move on. Skyrim's crappy script tool, Papyrus, is proof positive that the old adage that 'computers always do what you tell them to do and nothing else' is horseshit. You can ignore this advice, but your install will be ten times more stable if you keep it light instead of bogging it down.
6) Before downloading a mod, look at the comments and the dates involved. If the comments seem to be full of people having trouble, do yourself a favour and move on.
7) If you want loli/shota, google is your friend.
8) Do not touch or interact with weapon racks. They are the devil.
9) FNIS has animation limits. Sexlab has animation limits. Don't just download everything, be a little selective. Personally, I find funnybiz to be a large pile of low-quality space-waster, but you can always selectively remove animations you don't like.
10) A pirate copy is perfectly fine and modding it is perfectly fine. FNIS will throw a warning about it. It doesn't matter in the slightest. If you have a Steam install in a nonstandard location, FNIS will throw a warning about it. It doesn't matter in the slightest.
11) Understand that Skyrim's natural state is 'a bit fucked up'. If something isn't working right, google it first, and try reinstalling the mod. Check for clashes with other mods by clicking it in MO, it will highlight interfering mods in green or red to show overwriting. Try putting it further down the load order. Don't be too finicky about fixing things if you can just live with it instead.
12) If you try to load a save and it just shits itself with a silent CTD, load the autosave that was made when you first created your character, then load your save.
13) Use an alternate start mod. ALWAYS make sure this mod stays at the absolute bottom of your load order. ALWAYS.
14) Don't use mods you don't really want. The more you add the more likely everything is to explode.
15) Don't uninstall mods after you've started playing. The scripts will hang around in your save.
16) Download the mod 'Haven Bag'. It has various craftstations in it like a grindstone that you can use to reset your camera when it inevitably fucks up and gets stuck in third person mode.
17) If your quicksave starts taking ages to save/load, make a hard manual save and delete the quicksave. Load your manual save and make a new quicksave. You can use MO to easily do this.
18) Follow Dariem's guide on page 2 of this thread. Including the bit about cleaning up with TESedit. Bethesda are lazy fucks, you need to clean up after them a bit or things will get glitchy. It isn't hard or time-consuming, and there are several text and video guides. Do it.