How to determine which neutral to which power?
Yes, it matters.   It is vital to pair the neutrals with their partner hots.  You should have marked the wires at the time you installed them, either by tagging the wires with tape, or by bundling the pairs with tape, or any other method that makes sense.  

Now, your best bet is to document carefully which outlets are on which hots.   Then, pull one of the neutrals off the neutral rail and insulate it.   Make sure that all the outlets on one circuit do work, and all the outlets on the other circuit do not work.  Now you know the still-connected neutral is associated with that hot.  Mark it! 

Do not allow a situation where some outlets on hot A return on neutral A, and other outlets on hot A return on neutral B.  That is a wiring defect that should be corrected ASAP because it will result in the neutral being overloaded.   Neutrals do not have circuit breakers, so the system absolutely depends on neutrals not serving two hots.