I have been struggling with the baking process as I had some issues to fix each time, like changing objects materials in order to not get intersecting objects as well as overlapping elements in the same material which didn’t allowed me to paint objects independently on substance as it uses the same UV space.
I have also had problems with the AO maps in elements like the tongue or the teeth as they were going to be an animable object, the teeth because the movement of the lips and the tongue because it should move but as it is the AO are generating artefacts. I decided to go on and fix the AO maps later in Photoshop.
Finally, I started to pain the Minion using fill layers and alphas in order to reuse the substance file to do new textures with different colours as well to help me tweak them to find the best result.
Then I started baking the alien leader finding new problems similar to what I had in the minion model and taking me also 2 days to have all ready to start painting the model. Finally, I started to paint it in the same way I did the minion using Fill Layers and alphas.
In order to put more detail I used combination of diferents smart materials tweaking the properties of them to get different results as well as using alphas to add textures using the height like on the tongue or the scars. I also used a brush with alphas in order to paint different textures for the skins to create a pattern of lines and give more detail to the skin.