.....so could I get say zone one to output to sound card one and zone two to output to sound card two?
yes you can .. and thats how you should be doing it. All audio configs are by zone. The default one called "Player" unless you renamed it is a "zone". You can also use zones for different configs (eg DSPs like eq or volume leveling in one zone and no DSPs in another) outputting to the same aduio device.
or.. have two instances of JRiver with JRiver one to output to sound card one and JRiver two (on the same PC as JRiver one) to output to soundcard two?
well I suppose it is possible, but if you are using the same "Library", you'd still have to configure the second audio output device. Running multiple instances at the same time on the same PC .. is pretty rare and is often just temporary for testing and things. Not to be confused with running multiple installs on different machines on your LAN.
read =>
https://wiki.jriver.com/index.php/Zones The word zone can be confusing ... although it can indeed refer to a separate "physical" playback area .. like in a new room, it doesn't have to be (I have 5 zones for audio playback, video playback and web streaming) Look at it rather as a separate configuration of an audio device, or a config of an additional audio device. Each install of JRiver can be used server, controller, and or renderer. You can even control remote zones from client PCs. Basically you can do pretty much what you want to ... with some limitations on certain DLNA renderers.
If you are just going to connect active speakers in a different room for example, this is easy. Just create a new zone, choose the second sound card if you wan to. You can even link the two "zones" together so they play in both rooms. OR the second room can have a client PC or a DLNA renderer of some kind. Endless possibilities, as your license includes multiple installs (if the are on the same OS, othe wise you need the master license).
Normally, you would have only one machine running media server, and only one instance of JRiver running (per machine)