You're not supposed to install it on emunand. Menuhax goes on your sysNAND. If you want custom themes on your emuNAND, you can install them in CIA format or install hblauncher_loader to emuNAND and use CHMM2. Neither of these things are done in dev mode.
If you have your boot.3dsx replaced so menuhax boots directly into CFW, then hblauncher_loader will do the same, and will obviously red screen because it's trying to boot into CFW when you're already in CFW (I'm now starting to think this is the issue you're having, but "it doesn't work" isn't really a lot for people to go on if you are trying to explain what you're having issues with, so I'm just guessing here)
If that is your issue, then
http://gbatemp.net/threads/ctrbootmanager-3ds-boot-manager-loader-homemenuhax.398383/ is your salvation.
With it you can choose if you want to boot HBL or CFW and it will autoboot CFW if you don't make a selection. That's the easiest way to have cold boot CFW while still being able to use HBL.