In principle, DXVetery runs fine with the Steam version of Deus Ex, there's just one file that's causing problems: DeusEx.exe. We explain how to work around this problem.
DeusEx.exe has a small but important task to fulfill: To start up the actual game. The Steam version of Deus Ex comes with a modified version of DeusEx.exe, one that refuses to run without Steam. DXVetery, on the other hand, does not run with Steam, so you need an alternative DeusEx.exe file. There is a free alternative DeusEx.exe file available. Replace your Steam version's DeusEx.exe file with that alternative version before installing DXVetery, and you should be fine. Make sure you backup any files before you modify or replace them! UPDATE: The author of the alternative Deus Ex launcher has given us permission to include his launcher in the DXVetery Setup. The latest version of the installer automatically detects the Steam version of Deus EX and installs the kentie.net Deus Ex launcher for DXVetery.