Don’t really have anything specific to recommend in that respect, sorry. Never tried it, so I have no clue what might work best.
On a sidenote: for games with native SBS 3D support you are best off creating a new profile based on one that handles SBS input (e.g. Rise of the Tomb Raider for DX11). For a bunch of reasons directly hooking into a game is always better than using desktop capture later.
To make that easier I’ll add a profile template for games with native SBS 3D in the next vorpX update.