The Level-2 files for MODIS contain sufficient information for accurate geolocation. No external geolocation file is required. SeaDAS can overlay coastlines and grids, or reproject the files into any number of coordinate frames.
If you are having problems geolocating the Level-2 files in SeaDAS, please post to the SeaDAS forum with specifics on the error you see, and they should be able to help.
The Level-1A files, however, are in the native format formerly known as MOD01 or MYD01, which does not contain sufficient information for geolocation. If you want to view L1A or process L1A to L1B or L2, you will need to create a geolocation file. For a discussion of that process, see:
http://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?tid=106-- bryan