How to determine which of 2 common/neutral wires belong to my hot wire
I turn on every possible load, and put night lights or something into every receptacle.   Then I start back at the panel or wherever I have separated conductors.     I unhook all hots and neutral going into a particular conduit. 

Then I measure the resistance of each hot against each neutral.  I aim to see a simple answer.  If I do not, then I troubleshoot the crossed neutrals until it is simple.  Then I tape those pairs together where they enter.  Without this first step, the potential of a crossed neutral will make everything else hard. 

If I was at an intermediate point, I then hook up one pair of wires going back to the panel, and go to the panel and test out which pair it is.  Again with the tape.  Rinse wash repeat.  

I won't bother marking wires in conduit if it's obvious; like a 12 AWG MWBC blue-blue-white and also a 10 AWG heater run red-red.