You will need to fill each side separately. The fuel lines are large enough to supply the engines, but not large enough to allow the fuel to transfer from one side to the other and equalize while fueling. Also, the fuel levels in the two tanks will not equalize if your boat is not sitting level.
The fuel system has 3 valves that allow you to separate the 2 systems (normal) by closing a "crossfeed valve", or run both engines from one tank if needed.
Your Owners Manual covers the fuel system description. If you don't have the Owners Manual, one can be downloaded from the
www.FourWinns.com website. Click the "Owners" tab. Select your year and model. You will also find performance specs in the "Fast Facts" section, the on-line parts catalog, and other info.