Sloop, here we go with Scenes 101:
1. Scenes are are simply a group of devices. Scene is equal to a group in INSTEON vernacular
2. Each device in a scene can have its own on level and ramp rate regardless of its local on level and ramp rate. Example: If you have a scene called sloop, and you drop in slooplinc1 and slooplinc2 in there, then you could assign:
slooplinc1- on level 50%, ramp rate 2 mins
slooplinc2- on level 70%, ramp rate 5 mins
So, now, when you go to your computer and click on the "sloop" scene node (on the tree to your left), and when you press the "on" button, then slooplinc1 is going to "start" turning on to 50% which should take 2 mins
slooplinc2 is going to "start" turning on to 70% which should take 5 mins
If you click on "fast on" or "fast off", neither the ramp-rate nor the on levels apply.
3. Now, let's go one step further. Let's assume that now you are going to drop in one of the KeypadLinc buttons into the sloop scene. If this is a the "load" KeypadLinc button, then you will be asked whether or not you want to make this button a "controller" or a "responder". If a "controller", then you can assign on levels and ramp rates for "slooplinc1" and "slooplinc2" in the same way that you assigned it for the "sloop" scene. The only difference is that now, instead of ISY, you can control slooplinc1/2 from the keypadlinc button you drop in
Now, with this out of the way, the answer to question 1:
If you already have all your devices linked in ISY, then you would never ever need to use the paddle press/set button on any of the linked Insteon devices unless you wish to reset them.
For your scenario, all you need to do is create a scene, and drop your SwitchLinc relays in there and both as controllers . This shall mimic your three way set up since each relay controls the other.
Whoooah ....
On to the next question (how am I doing?)
Question 2
Ditto (above). You would never ever have to ever never click on that set button unless you want to reset the device