Here's what I think we'll see this fall:
iPhone 6S
4. A9 system on a chip (SoC) with 2 GB RAM and faster dual-core CPU/GPU.
iPhone 6S+
4. A9 system on a chip (SoC) with 3 GB RAM and faster dual-core CPU/GPU.
Apple will not make 2 versions of the same chip with 2 different RAM sizes as the RAM is integrated in the SoC so we'd be speaking of 2 different SoC's.
I'd say both phones will have 2GB of RAM.