get the bluestreak animatin importer
extract all animations from marine.model_animations into data\characters\marine\animations
Have a look at some of them to get a feel for how it works. Overlays will look glitchy, because the importer loads them verbatim, instead of in addition to the base animation they're supposed to overlay.
replace or add to animations in data\...\animations folder. Then rebuild the animations tag with tool. I personally would make a new batch file from a text file with this text:
cd "C:\Program Files\Microsoft Games\Halo Custom Edition"
tool.exe animations characters\marine
pause
and save it with the .jm_ anims. Run that, and the tag is rebuilt