Why not connect everything to the same power pins?
Do you mean the sensors need different power AND logic voltages? Can you post a wiring diagram?
I see two mistakes here.First of all: there's no -3.3 and -5V available from the Arduino. Only +5V and +3.3V. I don't think I've ever encountered a sensor that needs a negative voltage anyway, so I'd be interested to know what special sensors you have that require a dual voltage supply.
Secondly: you don't run out of power pins, as there's nothing stopping you from connecting many devices to the same pin, provided that the total current they draw is what the Arduino can handle (which is not much, and also depends on how the Arduino itself is powered).
I am using an external power supply to allow me to reduce the noise.
I am using an USB interface to connect the sensor to the ADC and since micro USB has only 5 pins I am limited to 2 power outputs 1 ground and 2 differential signal sources.
This totally doesn't make sense. USB is a specific protocol, and it's definitely not analog.
Why don't you draw a complete schematic of what it is you're trying to do, plus a list of which sensors (with part numbers) you want to connect and how. There's less and less sense to this whole thing.