I am having trouble with changing the direction of the building that transports items between islands, specifically between the central and the bottom island, I'm attempting to send the items from the bottom island up to the central island but the building doesn't want to place correctly.

Hi Ryan.Mxn!
You can change the direction of the transporter containers by placing them in the blue circle on the island you want to move things to.

In the case you mentioned, you should be able to move things from the bottom island to the central island if you build the transporter container in a blue circle on the bottom border of the central island.

Let me know if it worked and feel free to ask if you need anything :)