those parts of gui can't be turned off.
tho you can disable some buttons in toolbar
also if you don't use fxp features, you can simplify gui by going to "View" menu, "FTP Only".
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Also, I don't see a favorites menu option with a list of sites. Do I really have to click on Sites>Site Manager everytime I want to connect to a site?
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obviously you haven't bothered to read online tutorial and/or included help file...or even mouse-over all the icons on toolbar :/ see that lightning icon? that's shortcut to your sites. see that star icon? that's where your folder bookmarks are.
if you do want to open Site Manager, just press F4.
i think you are the 1st user to complain about flashfxp's gui "bloat" since this forum was created :/ what resolution are you running? 640x480? :/