TG is absolutely right, ATW (both 3.0 and 6.0) are using its own sets of mod folders where the ATW specific files are located.
If your other RTW mods (none vanila RTW/BI stuff) are also mod-foldered, there should not be any problem.
If you have base folder file changes (like some altered RTW/BI files in the original RTW/BI folders, there might be problem, because both ATW mods still use some skeleton or animation files from the Vanila RTW/BI folder.
As long as these files in the RTW/BI folders are not changed, both ATW mods would still run.
[This message has been edited by ParthianShot (edited 10-20-2011 @ 01:59 PM).]