Are the bearing shells identical??? Are the oil squirt hole notches in both of the bearing shells or not...
I've seen bearing shells where one set has oil squirt holes and the other doesn't... Put the shell with the oil squirt hole notch in the cap and the one with no oil squirt hole in the rod if both shells do not have the notch...
If both shells have the notch for the squirt hole, then it doesn't matter...
When you look closely, the oil squirt hole is in the cap and not the rod, they usually machine a channel in the rod cap for the oil and not the rod, so you want the bearing for the cap to have the notch for sure...