It's not annoying for me. I keep it simple and install textures manually. I already had the Bethesda HQ packs installed through Workshop. I just downloaded the Skyrim HD files from Nexus and extracted them to a folder. Then copied the Skyrim HD data folder to my Steam Skyrim folder and said yes when asked if I wanted to merge them. Then said to replace the files in the conflict window that pops up. The Skyrim HD files simply overwrote Bethesda's and Skyrim HD doesn't even show in my mod list when I start Skyrim.
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I use a lot of Steam texture mods now - as shown in my post above. I am downloading the Full Skyrim HD mod now - I want to give it a try. Looks like they are packed using BSA? How did you extract it?
Once unpacked you just merged all of the files like said above?