I tried to run Carbonite (TomTom emulation disabled) and QuestHelper together along with TomTom when WotLK was still new and quest databases weren't as comprehensive for the new zones as they are now. I ended up getting confused with having two seperate arrows to follow.
In the end I found it's
much easier to disable QH (but keep it in the addons folder) and use Carbonite for the majority of quests. Where Carbonite was missing quest data I'd just re-enable QuestHelper for the duration of the missing quest, then disable it again. I'm not suggesting you do the same, but it worked for me at the time
Tip: It helps if you have something like Addon Control Panel (ACP) for managing mod loading without actually leaving the game space (though a reloadui is usually still needed).