New features implemented in the develop branch allow you to do what you want, i.e. define coupled weak formulas where unknowns can belong to different meshes, or even mesh types. These features will be included in the next FreeFEM release, which should come within a few weeks.
Here you can find two simple Stokes examples demonstrating this feature, where we use two different meshes for the velocity and pressure: FreeFem-sources/stokes_composite.edp at develop · FreeFem/FreeFem-sources · GitHub FreeFem-sources/stokes_periodic_composite.edp at develop · FreeFem/FreeFem-sources · GitHub
You will see that the syntax is a little bit different depending on whether you want to use the problem/solve syntax or the varf/matrix approach.
You can also find a volume/surface coupling FEM/BEM example here FreeFem-sources/Helmholtz-2d-FEM-BEM-coupling-MUMPS-composite.edp at develop · FreeFem/FreeFem-sources · GitHub but it is a little bit more involved.
The documentation for these new features should hopefully come soon.