the problem isn't that your circuit is built wrong, but that between every node you have an inductor formed by the wires you've used to connect everything together.
As you discovered earlier, the boot strap capacitor won't get charged if there isn't anything to pull the mosfet down to ground.
this will occur when you connect a battery across the output, if the capacitor gets depleted then you can't turn the mosfet on.
this is another reason why you should use a half bridge design, also known as a synchronous buck.
of course, you can connect a resistor and diode to the highside power supply, and place a 12volt zenar across the cap. but that's just one more milliamp of wasted power.
the zenar is needed of course to prevent overvoltage.
as far as what the bootstrap is referenced to, do a Google image search for 'highside bootstrap' and read the datasheet for the driver you have.
there should be no confusion about how to hook the circuit up.