Ok I think I see what is going on. You are probably confusing menuhax with the autoboot application.
The default installation for menuhax is to only execute the exploit if you are holding L. Any other time it loads the home menu normally (sysnand). Most people do a custom installation where menuhax executes the exploit by default and only loads the home menu normally if a button is held down during the loading process, usually a specific button (i personally use start).
Ctrbootmanager is actually separate from menuhax and can be used with any *hax exploit, it just happens to synchronize extremely well with menuhax for the automatic loading of cfw at boot. It also has its own recovery key that is separate (or should be) from menuhax.
Check the root of your SD card for a file called boot.cfg and open it with a text editor (notepad++ is idea, but plain notepad will work). Note the line that starts with "recovery = ". Check
here for a list of values for the various keys, and change the value after = to match the key you want to use. For example mine reads "recovery = 8;" because I use the R button to access the menu.
Save the boot.cfg file and make sure the updated version is on the root of the sd card and that all the other neccessary homebrew files are present as well (like boot_hb.3dsx).
Load into emunand normally and launch CN, delete your existing save and reinstall the payload using smea's ninjhax2 site and ensure you set the system version to match your Emunand, not the sysnand. Execute the exploit and once it starts executing (watch for the "homebrew ropbin" message) hold down the button you assigned as your "Recovery" key earlier. It SHOULD load the ctrbootmanager menu, and from there you can select the homebrew launcher as long as it already exists in your boot list in boot.cfg. If not you will have to use the menu and settings to add it.
Alternatively you can do what
@Pingouin7 suggested. I personally use CN because I actually play OoT and don't want to deal with the payload save potentially causing problems. (just easier this way for me)