You can hex edit the menuhax payload to launch something other than boot.3dsx. Use something like HxD to edit your menuhax payload, search for the "boot.3dsx" strings (Should be 2) and rename them to something else (Must be same length, so something like "abcd.3dsx"). Then, rename your CTRBootManager 3dsx to whatever you replaced the string with.This way, you can keep the HBL launcher as boot.3dsx, but still load CTRBootManager through menuhax.
This, of course, can be adapted to other entry points besides menuhax. I just assume everyone is using it...