Its not that hard to run multiple installs of DW.
I have twelve installs of RA, LWAMI, Alpha Tau, and a stock install of DW.
Which install of DW do you have (Steam, old CD, Strategy First direct download) and what are you using as an OS (win10, win7)?
I run Win10 (64 bit) and the Strat First direct download of DW.
My version of DW uses a utility file named LaunchDW.exe.
If I want to install a new mod version, I copy my whole (stock) DW folder, rename the main folder, then install the new mod. Each mod folder also contains a copy of LaunchDW.exe. All I need to do then is run LaunchDW from the new folder and it changes my setting in my registry plus it updates the file location my shortcut icon uses. It isn't elegant (I need separate folders for each mod install) but it works and its fairly easy to change mods when I feel like it.
