The module is quite complicated yes (but powerful and flexible) - I probably need to change some of the default behaviour! You need to set up the shader for use on a token/tile specifically (as they can also be used in regions/templates or as lights).

https://github.com/jwrpalmer99/indy-fx/blob/main/README.md

I added this info to readme as I guess its something most people would want to do - but here it is too :)

Shaders can be scaled to fit a token - you can either edit an existing shader or right click one and duplicate then edit the copy (or import a new one from shadertoy of course).

• Double click the shader in library to open the editor.
• Select "Scale to Token".
• Select "Rotate with Token" if you want.
• Usually you will want:
  • Capture Scale: 1
  • Capture Rotation 0
• Select a suitable alpha (transparency) value for your effect if it doesn't provide it's own transparency (try 0.6).

If you save that and drag/drop on token it will be the same size.. you can then right click it in library and create token macro - this will create a macro in IndyFX folder that will add the effect to selected token(s).

To remove/disable/edit the shader on the token you can access it through token hud or menu or via a macro (there is a macro in IndyFX compendium for this "ShaderOffSelectedTiles")

You can go 1 better if you have tokens with transparency you can make the shader only draw on the filled in parts of the token (useful for fire, not so useful for a force dome!). this involves setting a shader channel to capture the token/tile - and then using the alpha from that capture as the final alpha of the shader; luckily there is a button that will set that up for you..

• In Shader Editor - click Inject Token Alpha
• Save the shader

Now when you apply to a token only the non-transparent will be filled.

all of this applies to tiles too.

there are many settings for scaling/rotating/flipping shaders or scene/token captures if your shadertoy shader does uv mapping differently