PCIe mapping varies from mobo to mobo, though typically GPU 0 is in the primary x16 lane. However, it is static once mapped. Otherwise using a -d 0 or -G 1 would be pointless lol. Most if not all OC'ing software like Trixxx and Afterburner use the static map as well, so you could see how problematic a variable PCIe map would be if you have software that applies overclock settings at startup.
Yep, hot air rises lol. If you have enough space between the cards I would look at getting a PCI slot blower fan to help vent the area between the cards. I have this same problem on my gaming rig when mining, and installing one of those did help slightly.