Further investigation suggests you have used the ClassicWB.uae config within the download package?
I would ignore that, if you already had a working Workbench setup.
Here's a guide:
1) Create a New UAE Config
2) Pick Expanded A1200 setup
3) Give lots of fast memory or Z3 memory to it (a total of 32meg is good)
4) Check this works and load the "jumping disk" kickstart screen. If not, return to the emulator menu and manually select whatever Kickstart 3.1 rom you are using (although Kickstart 3.0 would also work fine)
5) under Hard drives, use ADD HARDFILE and select System.hdf as the first drive (DH0)
6) then add one more , with ADD FOLDER (wherever you like) as DH1 , with a label like "Storage" .... you could even make this your system Dropbox/Google Drive folder, so that you can share it across systems. (I do this regularly, plus it means my projects are constantly backed up)
6b) if you really want, add a third folder as a Harddrive for random stuff you download but are not precious about!
7) Unpack the previously provided AMOSPRO folder to your second 'drive' (folder) location, on your host machine (i don't know if you use windows or OSX tbh)
8 ) Boot your new setup, and fingers-crossed it will load fine.
On first load it might ask for a valid Workbench disk to be inserted for verification (it sounds like you probably have an ADF for this anyway) ... also if you have the full set of disks for Workbench 3.1, this allow you to get the most from the "install"
You might also get asked about a few other install questions... For now i would suggest the following selections:
iGame image pack: "REMOVE"
Colour Pallet: "Default 16"
Theme Option: "NONE"
Old Icons: "DISABLE"
Copper Background: "ENABLE"
StackAttack: "ENABLE"
AntiClick: "ENABLE"
FreeWheel: "ENABLE"
When it says it is done, remove the ADF and hit "reset"
9) When you make it to your new workbench setup, find your way to CLI prompt (There is one on the desktop called "SHELL")
check that AMOS Pro is where you think it is, with
CD DH1:
DIR
hopefully you'll see the AMOS_Pro Folder mentioned before
ED s:assign-startup
add the assigns to this, and then use Escape, then X to save and exit (i have changed the second line to fit this tutorial)
;BEGIN AMOS Professional
Assign AMOSPro: DH1:AMOS_Pro/ >nil:
Assign AMOSPro_System: AMOSPro: >nil:
Assign AMOSPro_Accessories: AMOSPro:Accessories >nil:
Assign AMOSPro_Tutorial: AMOSPro:Tutorial >nil:
Assign AMOSPro_Examples: AMOSPro:Examples >nil:
Assign AMOSPro_Productivity1: AMOSPro:Productivity1 >nil:
Assign AMOSPro_Productivity2: AMOSPro:Productivity2 >nil:
Assign AMOSPro_Compiler: AMOSPro:Compiler >nil:
Assign AMOSPro_Extras: AMOSPro:Extras >nil
;END AMOS Professional
reset again, and then click on the DH1: drive, AMOS_Pro folder and try launching...