Extract your Maelstrom engine and copy the DirectX9_64bit to wherever you want your install to be located. Rename this folder Age of Pirates 2. Extract the contents of the Eras 2 pack to this folder. You should see your Program folder next to the modules folder in the directory. The save folders should merge. You should also see your Start.ini in this directory same as the Config.exe.
Run the config.exe
Setup the settings to your liking and hit Save & Play to launch the game. Create a short cut to the Maelstrom.exe and rename the shortcut to Age of Pirates 2. Copy this shortcut to where you have your games kept and run that from now on to launch the game directly.
In the future when you want to update, copy the save folder from your directory to keep your saves. Repeat the above process, then put your save folder back in.
Bonus.
Open Start.ini
Under “[sound_aliases]” add this line under the other items
soundAliasPath = Fantasy\
Save and close
Open config.exe, and change your Sound Scheme path to Fantasy, save and play