Using the geomembrane in a slope model gets complicated and is based on the problem you want to solve.
For slope stability and interface friction angle you set up an idealized case with the height of slope you are looking at.
For global stability you may want to put in 2 piezometric lines, one for the membrane lined materials applying its own phreatic condition and the second phreatic line for the foundation materials.
If you are relying on the membrane for strength, you would need to model the material with a built in reinforcement tool in the software, looking at the strength at failure and determining when that will be for the membrane specified.