Hello again,
I found the script I was looking for here: http://www.playonlinux.com/en/app-1799-Age_of_Empires_II__The_Age_of_Kings.html
And as I was suspecting, the script is not programmed to handle the layout of the Ubisoft Edition. The following shows the layout of the Ubisoft Edition. Files under FR/SP/UK are basically the same as the DE files.
.
|-- AOE1
|   |-- DE
|   |   |-- DIRECTX
|   |   |-- DOCS
|   |   |-- GAME
|   |   |-- GOODIES
|   |   `-- SYSTEM
|   |-- FR ...
|   |-- SP ...
|   `-- UK ...
|-- AOE1ROR
|   |-- DE
|   |   |-- Docs
|   |   |-- game
|   |   |-- Goodies
|   |   |-- Patch
|   |   `-- Sampler
|   |-- FR ...
|   |-- SP ...
|   `-- UK ...
|-- AOE2
|   |-- DE
|   |   |-- DIRECTX
|   |   |-- DOCS
|   |   |-- GAME
|   |   |-- GOODIES
|   |   `-- SYSTEM
|   |-- FR ...
|   |-- SP ...
|   `-- UK ...
|-- AOE2CONQ
|   |-- DE
|   |   |-- DOCS
|   |   |-- GAME
|   |   `-- GOODIES
|   |-- FR ...
|   |-- SP ...
|   `-- UK ...
|-- GAME
|   `-- AVI
|-- Manual
`-- Music
Adapting the two lines in the script that deal with checking if the right CD/DVD is present, I was able to install and play the game as expected. If you need more information don't hesitate to ask.