For a stacked, wedding-style cake (1 layer cheesecake, 1 layer red velvet), which cake would you stack on the bottom (using dowels+rounds)?

I agree with jmburns. I typically use straws (regular drinking or bubble tea) instead of dowels per Rose Levy Beranbaum's instruction. I also like to use foam core to cut my rounds. It's light weight, and pretty durable.

I would use the cheesecake on the bottom because of the weight.