Yes this can sometimes be a concept difficult for a beginner to get their head around. An isolated (transformer coupled) fixed DC power supply just supplies current at a specific potential (voltage) difference. The concept that it is a + or - DC supply all depends on which terminal is going to the circuit common of the application circuit.
So for say a general purpose analog op-amp type circuit requiring both positive and negative voltages and a circuit common, one can use two identical isolated (transformer coupled) power supplies. One supply would have it's positive terminal wired to the breadboards common (ground) connection and the other supply would have it's negative terminal wired to breadboard common. The opposite terminal on each power supply would become the circuit negative and positive voltages respectively.
This does not apply to non-isolated DC power supplies where one terminal is hardwired to a power common, (or neutral) connection and you are not free to swap polarities simply reversing connections to your application.
It looks like you are drawing a P-channel Mosfet. That has an intrinsic diode from drain (anode) to source (cathode). The top circuit should not have worked, becasue the diode would be forward biased and always on.
The bottom circuit is the correct orientation, but you may have problems turning off the gate with that configuration.
Im sorry error in the diagram...both the mosfets are Nchannel mosfets...IRFP460....ok so for the bottom circuit i have to run it using a P-channel mosfet if i provide a - voltage ...
and for the top circuit i have to use N-channel mosfet if i provide a + voltage
If the bottom circuit's mosfet is N-channel, then its diode is forward biased. To avoid getting a lot of confusion going here, I think you need to redraw the schematic you intend to use, including the gate drive, then proceed with trying to make it work.