I am using BES for my corporate email and BIS for my Hotmail. Is there any way to have separate folders for these 2 accounts so that I can access each account separately?

You can only have folders on your BES. BIS accounts (regardless of account type, i.e. Hotmail, POP3, IMAP, etc) do not support folders.

No,I mean separate folders on my Pearl home screen- aside from the generic "Messages" folder

You can't.

And please don't double post.