I have stacked a lot of buildings on my homestead. Although, I was from trial and error at first. I hate to say it, because I <3 you all so much, but the details on how to stack are a bit confusing, not just for me, for others too. If you don't mind, here's a simplified version of your instructions.

First, you select the move tool, then click on the building you want double stack, lets say you want the bank on top of the general store…you click the store, move it but dont set it down anywhere, then go to the tools, all while the store is still in 'move' function, then select the arrow tool, this SHOULD put your store in limbo, where it is moved, but doesn't belong there, just somewhere on your screen, then you move your bank where the store was, or if you want half way on/half way off where the store was, then refresh, they now should be stacked. 

Once you get the hang of it, you can also stack animals and decorations on top of the buildings too.

*example, I have a pine tree on top of my orchard; wooden carved statues on top of my land office. Also, non-rideable horse stacked on top of the big barn and a chicken on the deck of the saloon.*

when i click on chicken coop with move tool and dont sit it down and click on the arrow it just puts my coop back where it was, what am i doing wrong already?

confusing..agreed

but what does it do to being able to collect on the building bonuses, etc?

 I would love to see your homestead!  Any chance?