When you get that new pair of running shoes, do not immediately start to run in them. Walk around the house for a few days in them and wear the shoes when running errands around town. Wear them to work if you're allowed. This will also provide a good snapshot of how your new running shoes fit. If the new running shoes do not feel right when walking around, they definitely will not work for you during a run.
Phase Them in
Now that you have worn them around the house for a few days and they feel good, you need to actually start running in the shoes. Phase the new shoes into your running routine gradually. For instance if you typically run five days a week, use the new shoes for only a day or two for the first two weeks. Then, gradually increase their use until the new running shoes are used for every single run. This gives you a chance to make a real life comparison between the old shoe and the new shoe. If there is any noticeable change in foot discomfort during this phasing in, you may need a different pair of shoes.
A Perfect Fit
Running shoes should fit great from the moment you put them on. Don't expect the break in process to cure any problems with the way your shoes feel when you first try them. The purpose of the break in process is to prevent problems with great fitting shoes, not to overcome problems from ill-fitting ones. A person should not just buy any pair of running shoes off the shelf. Locate the nearest specialty running shoe store and have their personnel diagnose your foot composition, running motion, and how that motion affects your feet. If the shoe does not feel comfortable or causes pain, then do not bother hoping it will feel better after you break it in.
Take Breaking in Notes
Make note of any particular problem you had with new running shoes during the first few break in runs. This way when you go back to the store or visit your foot doctor, you can relate exactly what the problem was with the particular shoe. It really does not help if you tell the shoe representative that they just did not feel right. For instance, if the arch of your foot hurt after a run, then tell them exactly that and it will go a long way toward finding the right shoe for you.
Pay attention to other parts of your body besides your feet when breaking in a new pair of running shoes. Too many times people only take notice of how their feet feel when breaking in a new pair of running shoes. The feet connect to the rest of the body and if your back hurts during the time you are breaking in the new shoes, then it might be the shoes, even if your feet feel fine.