You have to think like water... Remember that water can WICK around things and behind things and UP things.
Your flashing should work like this...
BELOW the ledger, the flashing should go at least 1" behind the ledger, and extend at least 2" below the ledger and on the OUTSIDE of your top course of siding. The bottom edge of the flashing should have a small bend away from the house at about a 45* angle. This is called a drip edge and discourages water from going around the flashing and wicking back up behind it.
ABOVE the ledger, the flashing should be BEHIND the bottom course of siding, at least 3" and should extend over the top of the ledger. It can sit on top of the ledger and extend out onto the joists a bit, and this isn't bad because it limits the amount of water that gets into the endgrain of the joists.
OR You can bend the flashing down over the ledger, then butt the joists up to it.
There is a great product out on the market now called a pneumatic palm nailer. It is a little smaller than a palm sander, and has a head with a magnet in it. You stick your joist hanger nail in the head, set the tip inside the hole, and push. Ratatatatatatatatatat!!!!! The nail is in there with hardly any effort in about 1 second. Very Very Cool!
A compressor and a framing nail gun are great to have as well, rent them if you can't find one to borrow. The palm nailer is only about $60 and worth every penny if you have a compressor.
Be aware, that joists can vary in dimension by as much as 3/8". This can make it hard to build a flat deck. Just to be safe, you might rip all your joists to the dimension of your narrowest joist, so they are all the same. Paint some treating material on the raw edge and place the raw edge down. When you do this, keep in mind that the joists tend to have more or all the knots on one edge. That edge should be on the top when the joist is installed. If they are on the bottom, the knots fall out, and the joist isn't as strong.
USE PRESSURE TREATED LUMBER ON YOUR DECK FRAME. CEDAR WILL ROT EVERY TIME!!!!
I can't tell you how many decks I've replaced due to rot, simply because they keep building them with hemfir or cedar frames. sheesh!
Good luck on your deck, have fun with it. feel free to email or post back with more questions...