[Pisces]

DW (and SC) keeps some registry keys in the Windows Registry, among which several paths where parts of the game can be found.

In a 32bit Windows it is found with at:
HKEY_LOCAL_MACHINE\SOFTWARE\Sonalysts Combat Simulations\Dangerous Waters

or for 64 bit Windows:

HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Sonalysts Combat Simulations\Dangerous Waters

The paths found in keys in there must be changed to the correct location every time when you switch between the modded games.

You can search, read and modify the registry entries with the Windows program Regedit.exe. Just open the registry on the left side by unfolding the tree until you reach dangerous waters. Eventually you will find the registry keys with the paths in the right panel.

WARNING:
As modifying the registry can have serious consequences when you mess it up I suggest you do not change anything in it. It may break your system. There is a method of importing and exporting specific sections of the registry from/to a small .reg text based file. But I do not advise trying this if you are unfamiliar with changing the registry.

Instead a safer method is to rename the folder of the modded game you wish to play as is listed in the keys of the registry. Give the folder of the mod that you do not want to play a different, but still descriptive name.