When using CLR to clean your toilet you should leave the CLR in your toilet for at least 2 minutes.
However you can leave the CLR in your toilet for 10 to 20 minutes and then scrub the toilet down and flush the toilet a few times.
When I use CLR in my toilet I allow the CLR to stay in the toilet for 10 minutes to give it more time to work on removing the stains and calcium deposits.
Then I scrub the toilet with my toilet brush and then flush the toilet a few times.
After that I use my regular toilet bowl cleaner to clean the toilet bowl some more and flush the toilet again.
CLR Calcium, Lime & Rust Remover should be applied directly to the stains in the toilet and allowed to sit for a few minutes at least and then scrub the toilet.
The longer you allow the CLR to stay in the toilet the better it will clean.