Every quest i do i have to open quest log and shift click the quest so it doesn't show a second time from the blizzard default tracker. Can i disable that?

Go into Questie Options --> Tracker and make sure you have "Enable Tracker Hooks" checked. That should hide the default blizzard tracker and the default Questie tracker should appear. We're working on a new and improved tracker for version 6 here soon with loads of new features and QOL improvements. Stay tuned!