I use command line.

My workflow is like this:
FFMS2 (source) ---> Vapoursynth (video editing scripting language) ----> x264.exe
If I do need to use a GUI, I use MeGUI.
My x264 is self compiled as well. Although Komisar's builds are better than mine, I like the feeling of using something I compiled myself
You could probably manually replace the x264 executable in those programs that you are using. Look for the x264.exe file inside their folders, and download it from either x264.nl or
...::: Komisar x264 builds :::....
The AVX2 instructions are already committed to x264. You can check Dark Shikari's git for details:
https://github.com/DarkShikari/x264-devel/commits/master