You need to.
1. Delete water form ADT by savinf in noggit
2. Use Mjollnas ground doodad fixer after you texturing is done.
3. Creat your doodad set in the DBCs or search an ID of a set you like
4. Use the ground effects CMD tool to add this ID to your ADTs texture layer you want to have this set on.
All tools are included in the tools/cmd folder in my modding pack for the tutorial.