well, they are not in .at3 format or .oma format, they are in .msa format. it creates two folders on your MS root, CONTROL and HIFI. In the CONTROL folder there is a subfolder called PACKAGES. In that folder there are subfolders for each song (but not with the song's name as the folder name) with a .xml file in each of them made for each song. then there are countless other files that it creates in unknown formats.
unless you can figure out the very complicated and strange way that sonic stage puts them on there, I dont think it is practical to do it by hand. I would suggest just using sonic stage because it is rather confusing.