-When exporting your character, select the "mesh_root" object from your scene and delete it. (Also don't forget to check the export animations option when exporting)
-Launch assimilate, BUT add your ROOT.xsi model and double click on it (where it says single-player mode)...check "Keep motion bone" and "make it's own skeleton" change the path to "models/players/_humanoid/"the name of your new animation" dont name it _humanoid.gla!!!!
-You can also change the path so it points to your character dir (just make sure you remove c: )
-Next go to the "frames target" option (press + on the folder...) hit clear where it says ROOT do not change anything else (for now...maybe experiment later). If that worked you should see your new animations in modview.
If you want to make multiple sequences, you will need to outpout them to separate XSI files and batch compile them into a .GLA sequence, i don't have the details but it should be in the 2nd SDK .car files? or some released animation pack on http://jediknight3.filefront.com/