AFAIK you can check out both.
While PRS+ is based on the original sony firmware, adding some missing functionality to the UI and brings some (homebrew) Apps like Sudoku, Mahjong, Fiveballs and a Calculatur, but sticks to the original FW viewer-programms.
Ebook Applications is a whole new set applications NOT based on Sony-original code.
While progress goes fast, and Ebook-Apps is offering some additional file-formats to use, it seams to be in an (early) beta state.
If you install first PRS+ (appending the Sony-FW) and then Ebook-Apps you should be able to choose at each startup which application to use. (And if starting your reader attached to an USB-Port, and choosing Sony-FW, even without starting PRS+. So you will have the original unchanged FW.)
Last edited by Mark Nord; 12-26-2010 at 03:15 AM.