I don't use the Reader for PC software at all so I can't advise on that. However, you can transfer your MP3 folders using simple drag/drop to the PRS-T1 directory [drive:]
\Sony_Reader\media\audio using your op.system File Manager.
I suspect the reader will get its Artist, Album, Title and Track info from the Tag info inside the MP3s, rather than from the filenames/directories. So you may need to edit the Tags yourself before you copy to the reader. The MP3Tag freeware program is very good.
You should also be able to delete MP3s directly using your op.system.
P.S. Welcome to MobileRead