How to center a quick release rear wheel regularly
There are two types of rear dropout, ones that are vertical and ones that are horizontal.

With vertical dropouts you put the gears in top at the back and low at the front. Then you put the wheel in. Then you put some weight on the seat and fold the quick release lever over, applying whatever adjustment needed to get the quick-release tensioned correctly. The lever should fold up rather than down, forward or back as you don't want passing vegetation or other cycles to come into contact with the lever.

Horizontal dropouts require pretty much the same procedure however you have the problem of making sure the wheel is equidistant to the chain-stays. This is best done by having good eyesight and holding the wheel in place whilst you fold over the quick-release lever.

More generally you have a time penalty each and every time you lock/unlock your bike. You may want to consider investing in a cable loop to go through your D-lock and around the back wheel. These are affordable and need be not that bulky as someone is less inclined to saw through it to get your back wheel than they would be if they were able to get your whole bike. It will deter the casual rather than the determined thief.

The other option is to get a set of replacement quick-release levers with Allen key or 'special key' heads. In the UK these need not set you back more than fifteen pounds for the simple Allen key versions:



The 'special key' versions are worth the premium because you need more than an Allen key to get them undone:



These are a lot cheaper online, you can get the set for all of £8 if you Google 'Trans-X' quick release skewers.

the only pain with them is that the key needs to be carried and that does not fit onto a standard keyring too well.