Welcome!
"Can you grow plants with the pots stacked on top of each other?"
Yes!
"How much time does it actually take each day to take care of them?"
It depends on how many you grow
If you've got potions and a water pitcher ready to go, you should be able to zip through quite a few in just 5 minutes...I've had maybe 150? or more, growing in a house at one time - that takes longer
"How do you use fertile dirt? What difference does it make?"
To use fertile dirt, double-click your plant bowl, then select a pile of at least 40 fertile dirt - it takes 40 pieces to "fill" one plant bowl. Then, plant and tend your seed as you would with regular dirt.
Fertile dirt gives your plant a small chance to grow faster than it would if it grew in regular dirt. The plant gets a chance at one extra day's growth each time the plant's growth check occurs (for plants locked down in houses and at least 24 hours old, this happens at server-up - for plants in banks, beetles or backpacks, happens when your char logs into the game but only once per 24 hours.)
I save fertile dirt for special situations, like if I get a white mutant seed I want to grow out as fast as possible, for emergency plant orders from a customer, etc. I haven't used it in a while, but I remember usually being able to grow a fertile dirt plant one day faster than a regular-dirt plant, maybe two days faster, but never faster than that...
