I guess you could modify a USB cable*, or build your own special USB cable with no power connection.
You're probably OK with both power supplies connected. I think this is how the Arduino works when you run it from ~12V, using the on-board regulator. If I've got the board running off a 12V supply and nothing bad happens when I plug in/out the USB.
Now, if something horrible goes wrong with 5V (home built?) 5V supply and it starts putting-out 12V, you might blow the Arduino and
your computer's USB port.
* Cut it apart and ohm-out the wires to find the 5V wire, then re-connect the other 3 wires. (Somewhere, I've got a USB cable that we cut apart so we could measure current. It's ugly, but it does the job.)