Yes, DO NOT use the quick-release to position the wheel between the pads. Shove the wheels ALL THE WAY up into the dropouts and clamp the QR lever down TIGHT.

Misalignment of the wheel between the brake-pads can be caused by a number problems:

1. brake-caliper not rotated to have centerbolt centered on fork & frame

2. brake-caliper springs weaker on one side than other. This is caused by ADD/rushed mechanics using a punch to bend the spring on one side to center the brakes. This is a quick & dirty way to do it, but causes other problems in the future.

3. brake-cable too short can cause one arm to be pulled to one side.

4. wheel needs truing. That is, the rim will move side to side between the brake-pads when you spin the wheel. This is fixed by adjusting spoke-tension

5. loose wheel-bearings can cause similar symptoms to out-of-true rim. Best to check & adjust the bearings 1st to verify they have no play.