assuming that the panels are both
http://www.beyondoilsolar.com/Sharp142.pdf , it should not matter.
You solar array's are actually small enough that you could run all the panels on a single controller so any combination should be fine to try out. As it is now, during the day the reported input and output values should be close between the to chargers and would provide an excellent way to see if there is issues with a string or panel. You can also used the history information from the mppt units to see how close the daily generation is.
This assumes that your in bulk charging, once the unit goes into absorb or float, its very likely one unit will out perform the other as not all the available energy can be used