What's the best way to set up multiple render passes of a shot in Movie Render Queue?

Hi - I have a shot for film production with a few special render passes for use in nuke later (e.g. imagine “AllNoFog”, “FogOnly”, and actually a few more). The way I currently switch between these two render passes is I have a level subsequence, called “LS_Shot40_FogOnly”, which turns off all the other lights, hides unnecessary geometry, turns the fog on, turns on the fog specific lights on, etc… If that subsequence is inactive/muted then the shot renders “normally”, and if it’s active then the shot turns into a fog-only version.

The way we currently have it set up is we have a level sequence for the shot (called LS_Shot40_Master or similar) which contains subsequences (LS_Shot40_Anim, LS_Shot40_Layout, LF_Shot40_Camera, LS_Shot40_Lighting, etc., and this FogOnly subsequence is contained inside LS_Shot40_Lighting.

I can’t figure out how to activate or deactivate subsequences from inside Movie Render Queue. Which means I have to activate the Shot40_AllNoFog render item in MRQ, render, wait for it to finish, then deactivate Shot40_AllNoFog, activate Shot40_FogOnly, then dive into LS_Shot40_Master->LS_Shot40_Lighting and activate the LS_Shot40_FogOnly subsequence, and render again.

This works, but it’s not very clean. It also means I can’t, for example, just render the whole shot and go to lunch - I have to wait and render each pass manually (and this is worse if I want to render a bunch of passes for a bunch of shots).

Is there a better way to switch on and off “stuff” within Movie Render Queue?