You only need to worry about ADE if the book is encrypted with DRM. The free ones at SmashWords are not. ePubs are really a type of zip file, so there are several programs, including Sigil, that will let you open the ePub and make changes.
Sonys will open both LRF and ePub formats. They might display differently; I seem to recall that the LRF format did a better job on the 900s with right justification. Which format to download is personal preference, based on how you like them on the reader. Calibre will convert to and from ePub and LRF, so you can also download the ePub, make the corrections, convert to LRF and load on your reader.
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