In stash you can only assign a single funscript to a scene. I know there is a plugin for stash that adds ability to assign multiple funscripts to a scene, but it requires changes in MFP to support it. But I will probably add support for it eventually.
For now you could use Heatmap Generator (web), merge multi-axis scripts into one to merge multiple funscripts into a single funscript and assign that single funscript to a scene, MFP will unpack the funscript into multiple axes when reading.
Or even simpler solution is to add a script library under “Local” script repository and point it to a location where your scripts are. MFP will read the video file name from stash and use it to find scripts, which will load scripts for all axes.