Picked up my 2013 Saturday from the dealership,
Welcome!! And congrats.
got the two minute run-down on the bike and was handed the manual. Was a little unclear on how the FOB works in the case of emergency/loss, and reading the HORRIBLE manual that came with the bike hasn't made anything any clearer (Did they have to hire a dyslexic tech writer with no knowledge of English?).
Yep, the owner's manual is horrible. You would think they could pay someone that understands English to edit the damn thing.
As I think I understand it,
You will want to start searching and reading this forum, there are just tons of threads about the FOBS and such (and about the bad manual, and dealers who are clueless, etc)
the FOB enables everything when it's within about a yard of the bike (could be further). You can then turn or remove the start key that sits in the ignition. If you somehow miss the "low battery" alerts, and the FOB runs out of power, you put it on the clip behind the ignition switch and all functions fine until you can replace the battery?
Yep, that is correct. Placement of the fob if the battery is dead is tricky, and it will take more than a few seconds before it will work. You should try and practice it with the passive fob.
Why do they include a "spare" key in the fob, then? (and why is there one in the secondary, thin "spare FOB") Is that just if you somehow manage to remove the ignition key and lose it?
They are just being cheap. The passive fob, unlike the active one, contains no battery, so it has to be placed on the ignition to be used. The first gen C14 came with two active fobs, the second gen comes with one active and one passive. The huge stovekey thing in the ignition- most of use never remove that at all.
Where are you guys keeping the secondary FOB, wallet?
I keep it in my fanny bag that I keep in the luggage or with me. I keep the active fob permanently in my zipped riding jacket pocket so it is impossible to lose or misplace (unless I lose the entire jacket, which is unlikely). I had a regular metal key made by a locksmith to use with my bags (joined with the metal key for my helmet lock).
I'm guessing that if you leave home without the secondary, and somehow manage to misplace the big one, you're out of luck, even if you have one of the spare keys?
You don't ever want to lose all keys, or you are really SOL and have to get a whole new ECU! I wish they had included three fob/keys so I could leave one at home all the time.