It still conflicts with CFW Autoboots unless you use CTRBootManager
No, you just have to hex edit your payload so your menuhax points towards a different .3dsx file, while yellows8's launcher would point towards boot.3dsx as normal.
Keep your homebrew launcher as boot.3dsx, and get your menuhax payload to point towards anything else (4-characters long) in a hex editor by searching for "boot.3dsx" text-string and replacing it.
Then whatever .3dsx file you use to autoboot your CFW, you will rename to match what you changed the payload to.
Personally, I used nhax.3dsx
So when I start up my 3DS, it loads nhax.3dsx which is CTRBootManager, which loads rxTools code.bin
Then once I am on emunand, I can use yellows8's launcher, which will load boot.3dsx, which is my Homebrew Launcher.