Blackreach is, in my opinion, a criminally neglected part of Skyrim, which is a real shame, because it holds such potential. However, thankfully, mods exist! ...Unfortunately, very few mods touch it, and the ones that do can have compatibility issues with each other

Two such mods are The Blackest Reaches and Blackreach - Clockwork City 

The Blackest Reaches (TBR from now on) seeks to add more detail, more 'Glowy Stuff', more enemies, chests, ores, buildings, etc. to try and make Blackreach more interesting, both from a visual standpoint and a exploration standpoint

Blackreach - Clockwork City (BCC from now on), on the other hand, focuses on adding new landmarks and expanding/upgrading the central abandoned city structure, to try and live up to the hype it deserves, taking inspiration from Babylonian architecture while still keeping it inline with Dwemer feel, which it succeeds at beautifully, in my opinion

That's where this patch comes in! Designed to simply make TBR and BCC work together

For clarity, this pretty much just disables things that are clipping. There's a pyramid from BCC that clips into a structure from TBR, so i disabled the pyramid, there's a rock from TBR that clips into a brazier from BCC, so i disabled the rock, that sorta thing. Generally, i gave preference to the things that I felt added more to Blackreach. Navmesh wasn't patched, because i have no idea how to do that, sorry!

The load order i used when constructing the patch was;
The Blackest Reaches.esp (ESL flagged version, don't think this patch will work with the normal one)
The Blackest Reaches - USSEP patch (optional, my patch doesn't interact with this patch)
Blackreach - Clockwork City

If there are any bits i missed, please do not hesitate to mention! i am just one girl, after all, who is faaarrrrr too easy to distract with shiny. Constructive criticism is always welcome.

SIDE NOTE: there are some very minor visual issues in the original Blackreach - Clockwork City, but only one is accessible via normal play (specifically, one of the bridges is see through from underneath, which you have little reason to go under anyway), but that's outside of the scope of my patch, and outside of my experience to fix