QWINN'S THREE RULES FOR SUCCESSFUL MODDING:

Rule #1:  Place your patches as high in the load order as possible, meaning right after the last of its two masters.  Note that merging plugins makes such placement impossible, and thus should be avoided whenever possible.  Any exceptions I'm aware of, I'll mark them as "RULE #1 EXCEPTION" in orange below.  

Rule #2:  Make your installation order (left pane in MO2) match up with your plugin order as closely as possible.  Why?  Two reasons.  1)  The plugin list changes form records, and the install "priority" order will determine the winner of conflicts among the meshes, textures, scripts and other stuff that will be called on by the plugin.  A given mod needs the plugin, meshes and textures to ALL win the contest on *both* the install and plugin lists in order for the plugin to get the meshes and textures that it's expecting.  If you keep both lists in the same order, then by default this will happen naturally.  A different order could have one mod's meshes and textures win the conflict on the install side, and a different mod's ESP record win on the plugin side.  This is the #1 cause of the blackface bug and/or CTDs due to NPC replacers.  2)  It's also just easier to find stuff having them synchronized, rather than having to memorize where any given mod is in two different sequences.  Note that using LOOT for plugin ordering is utterly incompatible with Rule #2, as it will throw multiple plugins coming from the same mod all over the plugin list like a frikkin' tornado for no conceivable reason.  Manage your install and plugin orders by hand the way your favorite modding guide tells you and you'll be much happier in the long run.  Trust me on this.  Note that LOOT does remain very useful for indicating what mod combinations require patches - it's only the plugin order that I suggest needs at least some manual attention beyond what LOOT provides.

Rule #3:   Use Mod Organizer 2.  No other mod organizer comes even close in utility, ease of use, SPEED (it is insanely faster than NMM) or stability at this time.  NMM needs to be taken out into a field and shot and left for the vultures (can you tell it completely destroyed my complex installation by crashing in the middle of a large install - twice?).  I had high hopes for Vortex, but it's utter reliance on LOOT makes following Rule #2 more painful than its worth.

QWINN'S MODDING SECRETS, TIPS AND TRICKS

If you are ever trying to work with a plugin in the Creation Kit for whatever reason (even if just to convert it from oldrim to form 44), and that plugin has any ESPs as a master, the CK will completely break your plugin by removing all ESP masters automatically.  A way to get around this is to use SSEEdit to temporarily add the ESM flag (the same way you set the ESL flag on an ESP that you want to convert to an ESPFE) on the header of any ESPs that are set as masters of the plugin you're trying to work with.  Having that ESM flag set on the ESP masters is enough to get the CK to not disconnect those ESP masters from your plugin, allowing you to save it in form 44 or whatever else you need to do with it in the CK.  Just remember to remove the ESM flag from your ESP masters when you're done.  EDIT:  The mod SSE CreationKit Fixes by Nuukem fixes this problem and is highly recommended for this and many other reasons.

Obsidian Weathers includes "Fast Travel Speed Fix" (well, it's not setting the exact same value to the related game setting, but it's close, 3.6 vs. 3.4, the vanilla value is 1).  If you use OW, you really don't need FTSF, which has a form 43 subrecord anyway.

Place Ducks and Swans.esp and Relighting Skyrim.esp quite high in your load order.  I put them just above Cutting Room Floor.

Your other lighting mod (RLO, ELFX, ELE, or Luminosity) followed by Realistic Water Two really should come extremely close to the end of your load order.

(RULE #1 EXCEPTION):  Here's one situation I've found where it can be smart to move a patch out of it's Rule #1 placement  Take this mod:  Weight Overhaul .  It has a Books of Skyrim compatible version that, like BCS, needs to modify every single book formid in the game.  Now say you're using CRF and my BCS-CRF patch.  My Rule #1 would dictate the following order:  Books Covers Skyrim.esp, then Qw_BookCoversSkyrim_CRF Patch.esp, then WeightOV - Lightweight - MERGED - BCS.esp.  The WeightOV ESP would completely overwrite the patch in that order.  But if you load the patch AFTER the WeightOV esp, then the patch will correct the small number of records it needs to be compatible with CRF, while still allowing the vast majority of books in game to have their weight adjusted.  You won't have the weight changed on that tiny handful of books in the CRF patch, but it's a trivial number.  So in this specific case, moving a patch slightly lower in the order makes sense.  The number of cases where violating Rule #1 can actually help you is vanishingly small though.  Small enough that Rule #1 should still dominate in almost all decisions, because a patch can never *hurt* you if you follow Rule #1, the worst that can happen is that it doesn't help you, whereas they can make things much worse than having no patch at all if you don't.  Only violate Rule #1 if you know exactly why and what the tradeoff is, as in the case I just illustrated.

I recommend placing your audio mods (AOS and ISC) above WACCF.  Following Rule #1 will thus ensure the patches are ordered in the optimal way.

(RULE #1 EXCEPTION):  If you're using LOTD, AOS, WACCF and CRF (which would be my recommended plugin order for those 4), my default advice would lead to having the LOTD-CRF patch (called DBM_CRF.esp) be the last of the 6 patches needed by that combination of mods.  In this unusual case, though, CRF and LOTD are doing the same thing in their conflicting records (restoring the same cut item to the game) - therefore, I advise to move the DBM_WACCF patch down from where it should normally go and place it below the DBM_CRF patch instead.

The Pandorable NPCs-CRF patch and The Ordinary Women-CRF patch will completely overwrite one another.  You only need to use the patch for whichever of the two mods you've chosen to put lower in your load order.  As of v1.5.0, the same is true of the ICOW patches for these two mods as well.

If you're using CRF, AOS and WACCF, load my Qw_WACCF_CRF Patch after the Audio Overhaul Skyrim - Cutting Room Floor patch.  The change AOS makes to the conflicting record seems more like a fix than a tweak (it just changes the BlockBashImpactDataSet from "WPNBashBladeImpactSet" to "WPNBashBluntImpactSet" - duh, of course it should be blunt, it's a club!) so in future versions I will include it in my WACCF-CRF patch, and it won't have any significant impact (har har - see what I did there?) until then.