With high demand for the iPhone 6 and iPhone 6 Plus, getting your hands on one has been rather difficult. You could always order the phone from Apple to get it delivered to your door. Currently the iPhone 6 is available to ship in 7-10 business days, and the iPhone 6 Plus is available to ship in 3-4 weeks.
The other option is to check the store’s availability, and if the phone is available, pay for it online and choose to pick it up in the store. This could be a tedious process as there’s no way to see all the models that are available in the store, and you have to keep changing the model each time you want to check to see if it is available in the store.
There is a website, that will allow you to see all of the Apple Stores close to you and list all of phones they have available. This is a real-time list of the store’s inventory that gets updated every 60 seconds.