Your mods should still work even when launching DS from the Steam client. However, you can try this if you want to launch from Nexus Mod Manager: In NMM, click Settings. On the Settings panel, click the Dark Souls tab. Go to the Custom Launch Command box, enter the following: Command: C:\Program Files (x86)\Steam\Steam.exe Argument: steam://rungameid/211420 Close the Settings panel and attempt to launch DS using the Launch Custom Dark Souls button instead of the default button.