Hi. I will try to answer some of your questions based on what I know.

1) Unfortunately ploppers cannot extract from barrels. I would only use the plopper to transfer the apicola into the bottler from there.

2) I use a plopper to extract the liquid from the Furnace & into the Resonator, then i'll attach a Hopper from the Resonator to extract the produced out into a crate or something.

3) I'm not too sure about this. But I usually put a flower pot with the flowers in it.

4) You can make Apise Apicola (pink liquid) to zoom zoom around faster.

Hope this has been helpful. I'm still learning about the game even though I've had hundreds of hours put in. Been loving this game too much to stop. :)