Generally you simply set the avr for zone 2 (vs main zone) and then select the input to be used for zone 2...it sounds like you may be simply missing this step of selecting input while in zone 2 mode but not sure from the description (were you able to get sound out of the ceiling speakers and with what input did you get such?). I'd think this is something you could easily do from the front panel without a remote. I was thinking at first you had a digital input which may be restricted to main zone, but since you're using the analog inputs it shouldn't have such a restriction. Amp assign and input assignments might need to be checked as well.
One of the best sources for information is the manual, and while you may not need to know everything, they're generally good to get acquainted with. Older Denon manuals were known to be a bit hard to interpret (was even a guy on the internet by handle of batpig that created a Denon to English dictionary
). Remotes usually are the best way to control it/set it up.....are you using the graphic user interface with a tv or just using the front panel display on the avr?
You can still buy a Denon remote on ebay I'd think, or get a universal remote like something from Logitech's Harmony line....the microphone probably not particularly worth it but probably also available on ebay. It's always fun when someone leaves behind a whole home system without all the components or info on how it was setup....