I was using my boat for the first time a week or so ago.  While filling up the live well, it did not seem to want to shut off on its own, so I manually shut it off.  I am curious if others have experienced this same thing and question how to pump in fresh water.  Any suggestions?

That's how mine is. Its not an automatic pump, I have to switch it off manually or it will just keep pumping in fresh water, once it fills the livewell the water just goes out the overflow.  Every livewell I have ever had has been this way, and to my knowledge that's how most are setup.  The livewell switch on my dash also has an "auto" setting, but all that does it turn the pump on for 30 seconds every 5 minutes. I never use the "auto" setting though.  

 

That's a simple overflow set up.  Most modern bass boats are recirculating, and have a fill/drain/recirc valve.