I have been layering a 40F down quilt over my 20F down bag. I prefer to layer this way, as some wetness ends up on the quilt, which being thinner, dries easier/faster (when I get home–most of my 0F outings are one or two nights). Both are 800 fill, so I am not sure what I would do if both bags were the same temperature rating but different fills. Also, size is my very first consideration when layering. When I purchased the 40F quilt, I oversized it in length and width, so it wouldn’t compress the bag under it. In your case, I would figure out which one has more interior volume.
Back to fill, I think I would place the lower fill on top, in your case the 650, even though that bag would be heavier and cause some compression of the lower bag as opposed to doing it the other way around. The reason stems from pure ignorance. I fear that freezing down degrades it. If I am right, I rather replace the 650 bag than the 900 bag over time. I also read somewhere, I can’t recall how scientific the source was, that 900 fill is more affected by low levels of moisture than 650 fill. This was discussed at some point on BLP, but I can’t find the thread or recall the communal consensus…
Again, I want to be clear that I have no scientific basis for either of those statements on the last paragraph and that my experience with layering is limited to handful of happy, warm nights. I would actually love to hear from folks with actual facts about whether freezing down affects its life and whether 900+ fills are more affected by moisture than 650 fills.