If you have a wide roof box you'll probably want to fit it centrally on the roof. If you have a medium-width or narrow roof box they are usually positioned to one side, to make fitting and loading the box easier. You can fit a narrower box more centrally but you'll have to reach over a bit further to fit and load the box.
If you are carrying bikes (or something else) next to the roof box you'll want to fit the box as far to one side of the roof as you can, leaving you more space for the rest of your gear. If you have the choice between T-bolt fittings and around-the-bar (claw or U-bolt) fittings you can usually fit the box further to one side using the T-bolts. This is because T-bolts slide into the channel on the top of the bar so they will allow you to use the full length of the bar (around-the-bar fittings may clash with the roof bar feet).
Most roof boxes fit bars that are positioned between around 65-85cm apart, this does vary though. If you can choose where you position the bars on the roof then around 70cm apart is ideal for a roof box. You'll want to make sure that the box is positioned far enough forward to allow you to open your tailgate. An overhang at the front of the car is quite safe and normal and not something you'll see when you are in the car.