I use a combination of common sense, practicality and my own ears.
First, I take into consideration the room limitations. In my case, the room is the den which is shared by family and guests, so moving speakers too far into the room isn't practical. There's also a myriad of factors such as furniture, wife acceptance, aesthetics, overall room size, making sure speakers don't block the TV, etc. that affect proper speaker placement.
In my experience, it can take weeks or months to get the right speaker setup, and even an inch or two can make a noticeable difference. And to make things more complicated, speaker placement can change with any component or cable upgrade.