Welcome to the board Ed and congrats on the boat!
I've got a z17 but never really questioned fittings. I think the transom lower screened small is live well pump inlet and lower small non screened in drain (you must install manual plug on inside livewell drain unless you got optional valve controls at helm). The two starboard side ones include the bilge and livewell pump out (must pull the red valve out inside livewell to use) and lastly that larger upper transom may be the livewell overflow. I've read complaints that the overflow allows some water to enter the livewell when coming off plane and yes I see that even when I have manual plug installed in live well). I've also read some have a scupper valve installed to prevent the partial filling from the overflow. The partial fill doesn't bother me, even if not using live well I rinse it out at end of trips any way. Since its also not a problem after over 20 trips I'd rather not modify plumbing too.
You should have gotten several of the manual plugs, the same size is also used for cooler drain, I think they gave me 4 or 5. Oh yea, and that lower one with tethered plug is your main plug that must be in!
I haven't done much to mine other than use it as much as I can and oil/lower unit service but happy to try to answer any questions you may have. I came from a 2002 640lx w/90 so this is a step up but still easier to handle than say a z18 or larger. I didn't get hydraulic steering so still getting use to NFB clutch and also my 640lx with 90hp with stainless prop never had any prop slip it was a truly the 'water version of performance go cart'! I don't miss the smaller 640 size or storage but that one handled like no other in many ways.
Again welcome and enjoy!
Bill