The unzipping is done by launchpad's Shift-Shift-I sequence, so it is _not_ needed to do it manually. It would be the wrong target to unzip, too: When unzipping manually, the contents of the ZIP folder should go to the top level directory of the document partition (the Kindle "drive" on the host machine).
Duokan messes much more with the boot sequence, KindlePDFViewer doesn't at all (but Launchpad or Kite will, though). Having all that stuff installed at the same time is generally safe. I would not recommend to uninstall the jailbreak, though, but that's probably just personal preference. And "no need for jailbreaking" is only practically correct, technically both Kite and Duokan do jailbreaks, too.
Glad to hear you like the software :-)