but how do you do this?

 ! Quick Answer: Use the Background Color actor to create a 'canvas' that will fit all your stages in one.

Here is an example file create in Isadora 3.2.6

It requires for 1920 by 1080 video files as sources. (you can swap in any 4 sources of the same size).

NOTE: I use a Shapes actor to generate some 'sprite' and animation in this example, but if you wanted to animate an Image or Video (picture player or movie player) across the large canvas, I would replace the MultiMix (and shapes) with the Player (movie or picture) and another Matte++, again with 'scale FG' set to off. In that state it works amazingly as a compositor/animator of 'sprites'.

Haven't fully gone through your description, but would a virtual stage be helpfull?

Virtual Stage having the canvas of all other stages. All content/animations sent to this virtual stage.
'get stage image' -> chopper actor splitting to separate stages. (Maybe keeping this in a single background active scene)

What I have done is create a large Background

 Sorry, Ryan, maybe I'm being very stupid, but how do you do this?

I'm headed in the right direction!

 Great. Once you have the hang of it, it opens up some wonderful creative options.

@benju Is @DusX's method similar to what you used for Hexploitation?

I have done similar numerous times. What I have done is create a large Background that can contain all my stages.. if it's 5x 1920x1080 stages it might be  9600x1080. That configuration will allow me to place and animate an image across the entire canvas, usually I use Matte ++ and keep alpha on. I then use the Chopper actor to slice the large background into the discreet 1920x1080 feeds that go to a projector. 

Again with Matte, you can place this feed over your HD background (if using separate video feeds) and send it to a projector (specific stage).

If you have an arrangement that isn't as rectangular as 5xhd.. you can make a larger BG, with areas that you don't (only Chop out what you need)..  this allows for naturally timed animations between 'stage zones'.

Overall it's very flexible and can handle some complex configurations.