Scott - These are just my opinions. Take them for what you will. I am not a seasoned, expert free hand sharpener.
1) The main thing is to not store them in extreme environments. Don't let them freeze and don't sit them in the sun to dry. I put mine back in our basement when I'm finished sharpening and leave them on the workbench to dry. It could take a couple of days or more to fully dry, depending on the temperature. If you put them in a plastic tub of some sort w/a lid, make sure they're dry or you'll have condensation all over the inside of your container. Guess why I know that
2) Use the flattening plate when you suspect the stone is getting dished. If you hold them together and see any gaps between the two (usually in the middle area) then the stone is not flat. I'm trying to learn to use the entire stone when sharpening, not just the middle area, to help keep dishing to a minimum. Higher grit stones will not dish as quickly as lower grit stones.
3) Yes, use a pencil to scribble and "x" or some wavy lines across the entire stone. Work the flattening plate on the stone, rotating the plate or stone 180 degrees every so often to help keep things even.
4) The paste should last quite a while before you need to re-apply. When you feel it's not working anymore as it should, then you could reapply some paste. You don't need much at all, even on a new balsa strop. Less is more. I use a credit card or a putty knife with a good clean edge to spread the compound. Let it dry for a day before using.
5) Don't use both at the same time. Which one depends on how you want your jump from your sharpening stones to the strop, grit-wise. Personally, I'd be tempted to start with the 3 micron. It's not much of a jump from your 4K and will give you a nice toothy edge with some bite. If you like the idea of going from your 4K to a 16K equivalent strop, then get the 1 micron paste. That's doable as well. How refined do you want your edge?
Good luck and enjoy your sharpening journey.