Both have an eth1 through eth8, but on the 6700 eth1 through eth4 are 1g copper while on the 9700 eth1 through eth4 are SFP+ slots.
The bonds abstract all that away, though. Just make sure the physical ports aren't in the VSX cluster object's Physical Interfaces section, and create the bonds with whatever new physical ports you want. As long as your config only references bonds, you should be able to move from hardware to hardware with little effort.
If your Physical Interfaces section contains real ports like eth2 or eth1-04 and you're using them in VSs, you should look into 'vsx_util change_interfaces'. It lets you replace all references to an interface with references to another interface. Both must exist, and there will be an outage as the configuration is changed.