I usually wait 2 weeks for the color to settle. If the teeth were much darker than the shade you are lightening to, you may want to wait even a little longer as you will tend to get more rebound. Keep up your whitening once a week or so to maintain where you are at after the crown is in
Although I understand your logic, check retractors are not the best alternate. There are two reasons why this is happening. Either your trays are not made correctly because gel should not be able to seep through the top of the trays OR you are over filling the trays.