How to apply multiple beauty textures in the effects?

You can use multiple "effects"/ models together. If as an "effect" we can count any collection of .bsm2 models that has it's own materials, textures (if needed) and shaders used for them. If you want to organize different textures and different meshes in different folder inside one effect, all resources needed must be in one directory.
Beautification, for example, uses "!glfx_FACE" model spawned in config.js with retouch material and appropriate textures and retouch.vert and .frag shaders configured in cfg.toml file. Eyes or hair color changes use their own models and materials/shaders settings, which can be added to any other models/materials.
Good example of how to mix beautification with hair, eyes and other segments being colored is our "test_Recgnzr_All" effect, which can be downloaded from this page
Important thing to consider when you're trying to mix effect's models is the draw_order, which should configured in cfg.toml. For example, in "test_Recgnzr_All" in it's draw_order beside models' materials names you can find "!glfx_UPDATE_BG" commands, used to update glfx_BACKGROUND texture (used in hair, lips, etc. shaders) with current contents of the color framebuffer. If not to use it, some of the materials spawned can become invisible.
More examples and description of how to configure beautification you can find by following these links here and here