I recently bought RAM from a thirdparty vendor and faced the same issue/question. Well, initially not (for a day or so) but after I wanted to play some games in Windoes 10 on bootcamp (Battlefield1 and Dragon Age Inquisition, both using the Frostbite Engine) I faced some issues. Both games crashed to the desktop after 5-20 minutes of gameplay. This did not happen before I added the two new RAM modules and I changed nothing else.
I had 2x8GB original RAM installed in slot 1&3 and I placed the new modules into the slots 2&4. After I noticed the crashes I searched the internet and also found the apple instructions mentioned (https://support.apple.com/en-us/HT201191). But the guide doesn't mention anything about the correct slot usage.
Contacted the vendor and they told me that it would be best to use slot 2&4 for the larger RAM modules and 1&3 for lower modules. But of course all my modules were 8 GB - so equal size.
Searching the internet I found some sites suggesting that memory modules of the same type should be in the same bank.
I thought to give it a try and placed the original modules in slots 1&2 (bank 0) and the new modules in slots 3&4 (bank 1). After that change the issues with the game crashes were gone.
I know, its not a scientific answer with hard facts but I would still suggest this layout. Cannot tell if this is a good layout for dual channel mode though.