Layman's terms
Hello JeffS. Welcome to the Forum. Here is my attempt to clarify what some things mean:
None of your speakers are considered full-range because their frequency response does not extend from 20Hz to 20kHz which is generally taken to be the audible range of humans. Don't feel bad about this though; the vast majority of speakers aren't full-range, and even when they are, you still might not wish to use them as such, since a sub will almost always be better at producing really deep bass than front towers for example.
Because your speakers aren't full-range, they are classified as Small. If they had been full range, they'd be classified as Large. These classifications have nothing to do with a speakers physical size; they are merely definitions by which one distinguishes non-full-range speakers from full-range speakers. By telling your Yamaha Receiver that your speakers are all Small, the Receiver will 'know' that your speakers cannot handle the really low frequencies, and so automatically direct those frequencies less than the crossover frequency that you select to your Sub, which, as you will see from its specification, is more capable of handling lower frequncies than your other speakers.
You may note that your Sub still doesn't handle frequencies down to 20Hz; it only goes to 28Hz. This is also not something to worry about. Whilst it is true that your Sub would ideally handle frequencies down to 20Hz, it really is neither here nor there since your presently untreated room will be doing all sorts of strange things to the sound anyway.
As for the Yamaha's Crossover setting that you should choose, this is something you may wish to play about with. However, strictly, the setting should never be less than the highest lower-end figure from any speakers frequency response specification (120Hz in your case). If the Crossover setting was less than that, it would mean that you were still sending information to the speakers which they couldn't
accurately handle.
If you use the Yamaha's Crossover, then there is no need to use the Sub's, so that should ideally be dialled to its maximum so as not to interfere, i.e. 'confuse' the sub. However, in your case, with a crossover of 120Hz theoretically required anyway (due to the limitations of your speakers), this becomes somewhat academic.
As far as the +-3dB figures on speakers...
Ideally, a speaker should not add anything to the signal it receives, ie., the perfect speaker will simply pass the signal through without adding it's own signature. Unfortunately, no speaker is perfect, so the (by far) standard specification that speaker manufacturers state consists of a frequency range (say 110Hz to 23kHz) +-3dB. What this is saying is that over that frequency range, the speakers will 'only' add or subtract up to 3dB from the inputted signal (ideally it would be +-0dB but 0.5 is the best I've ever seen; on $63000 speakers!!!).
Phew! Hope this has helped a little. Enjoy your system

.
Regards