The copper is going to kill all the bacteria on your rocks. So it will help right up until EVERYTHING live on the rock dies.
No, it's not. Copper has some deleterious effect on bacteria, but it's barely noticeable in the real world. However, copper will kill off some inverts that are in/on your LR, so there may a spike when you start dosing - it's an easy confusion.Your LFS gave good advice regarding using LR, it's the best way to sort your situation.
Do *not* use Amquel or similar when dosing with Copper. The reaction makes the Copper 'more ionic' (I don't understand the Chemistry enough to be precise in terms), which can kill your fish at very low doses.
Do you have a power-filter in the QT? Or a powerhead? You need to get some flow running over the LR for it to act as filtration - after a while the powerfilter will pick up enough bacteria to do the job.
I'd highly recommend getting a Seachem Ammonia Disk - it's ideal for a QT (Measures poisonous Ammonia rather than total, not affected by Copper), will give you an ongoing alert about any issues, and lasts a year.
If you are going to use Copper to treat while the LR is still in there, you should be aware of 2 issues: one, that you shouldn't put the LR back in a reef tank - it will leach Copper. Secondly, you may find it absorbs Copper so you aren't getting quite the concentration you need - a Copper test kit (Preferably Salifert) will help with this.