Temperature stratification (or temperature layering), when the air near the ceiling of your vehicle is significantly warmer than the air near the floor, is common in vehicles used for nomadic living. (This happens in "sticks-and-bricks" houses too, but is more noticeable in vehicles.) For example, some nomads have reported water bowls for their pets freezing solid on their van floor, while they were at a comfortable temperature with their pets up in a raised bed.
To reduce temperature stratification, you can use fans to move air from the ceiling to the floor or from the floor to the ceiling.
When designing your HVAC system, consider putting your heat vents near the floor (since heat rises) or get heated floors, and if you have air conditioning, put cold air vents near the ceiling (since cold air sinks). You could also create a vertical circulation duct that runs from the floor to the ceiling with a small reversible fan on either end; this allows you to exchange air between the floor and ceiling as needed.
The vertical position of your bed matters too. A bed near the ceiling will be warmer than one positioned near or on the floor.
If the weather is nice, you can also mitigate temperature stratification through ventilation, either by pulling fresh air into your vehicle near the floor and exhausting it through roof vents, or simply opening all doors and windows to get your entire living space to quickly match the ambient temperature.