Since the 3.9 version of Amidock is a commodity, you could try running the commodities "exchange" program to see if it is hidden or running on the native Amiga resolution screen that has been hidden by opening a new Picasso 96-compatible screen or something like that.
Anyway, the dock is not as useful as you might think coming from a Mac background. I used ToolsDaemon to add menus to the top of the Workbench screen and an AREXX script that would translate ToolsDaemon preferences files into WB 3.9 AREXX commands. If I really needed a command, I could give it a keyboard shortcut in the menu.
