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.
The launch works!