I only use the Mega station, as it has 8 slots for dust containers, and can enhance all dinos that you tame. the little one can't enhance things like brontos, rexes, etc.

if using the mega one to do a smaller dino do you need to fill all 8 storage units or just 6

To enhance any dino, you actually only need 100 dust in one container.

right, the number of storage units is for aesthetics as well as being able to put multiple different dust versions in, so you only have to switch the template to modify a dino