Depends where you save your music. Hopefully not in your LW program folder. If the answer is no, then no problems. Not sure if LPE will install over the 5.5.9 version or not, either way not that important, you could always re-download 5.5.9 if you wished to return to it. We have links on the forum.

For Windows, I think the default download location for LW's downloads is:
C:\Documents & Settings\username\My Documents\LimeWire\Saved

LPE connects reliably, more-so than the regular LW. The regular LW you sometimes need to re-update the connection file.