Depending on the length of your new pump, replacing the existing fuel filter is a great place to stash it. If you do this, make sure your pump has a fuel filter on the input side, most of the little auto store pumps do.
I actually ran a new ground wire along with a 12V line all the way back to the fuel pump from the engine compartment, but you can just clean a spot on your frame for the ground and just run a single hot wire. You will want to use a relay to keep it from blowing fuses on your normal electrical system. Plus is just makes things cleaner. You can just run a line from the hot wire going to your coil over to the relay to activate it so the relay works when the engine is on.
Going into the engine compartment, just use the fuel line that normally runs into the fuel pump and re-route it to the carb. The fuel line is a little large, but just run two hose clamps and you shouldn't get any leakage. I might have run a new longer hose, but I can't remember.
As for the stock fuel pump, I just capped it off and left it. When I had a Triumph I made a block off plate like rascott mentioned.