I have separated the low poly mesh into two parts. The first is by mesh name and I use layers In 3DS Max to do this. For the purposes of baking, I first put all core 'areas' of the car into their own layer. Examples of this can be seen in the below right image. Then, within these layers, I detach assets so that no two items are touching and have a reasonable distance between them. I also separate them into groups that are mirrored and unique. This helps when it comes to creating the second full mesh as I know which parts need to have symmetry applied.
The second is by texture set. This is what will be carried into substance painter as the layers so I try to separate these out into logical groups. Example below left. In some instances, I have to use a multi-sub material. This is for when I've got two material sets across multiple objects that may be in different groups, and I have to apply the material at a sub-object level.
These are the colour groups across the car.
Below are screenshots of the UV's. These will be varying pixel densities once exported from substance painter.
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