Now, as you say, everyone has a way of doing things. This is how I would deal with the vinyl siding.
I would remove the vinyl siding where the deck is going. Depending on where the siding ends in this area, This is easy, you will need to unlock the siding using a "zip tool" (can be found at H.D. cheap).
This is probably going to be harder to explain than to do! But I'm in N. H. so, here we go.
First, you are going to have to know how vinyl siding is installed to know how to remove it. Vinyl is installed from the bottom, up. You are going to have to remove it from the place you want to start and work down.
The place you want to start is easy to find, the piece of siding that is under the door should have been notched out the width of the door. The cut for the notch will be hidden by the J channel.
If you go to the next interlocking butt above the bottom of the door you will be able to unlock it by placing the zip tool, curved side facing you, up under where the lock is, and appling a small amount of pressure, pulling down and tword you, this should release the panel.
with the zip tool between the unlocked portion and the locked portion, slide the zip tool in the direction of the panel next to the one your working on.
Go slowly and be carefull not to let the siding fold and make a mark. Do this on both sides of the door and the siding panel will release and you can unlock it from the panel below it by gently pressing downward. This will expose the nailing flange of the piece below it.
Once removing all the siding that is where the deck is going to be installed, You can go ahead and install the flashing, the deck joist, and again the flashing over the joist.
Now, depending on how you run your deck, will depend on how you put it back together.
I generally run my decking with the house so, I either use the decking to hold the bottom of the siding in place or use "sill trim". I would then reinstall the siding making sure it is going to line up at the top to relock the last piece.
You may need to buy a piece of J channel for around the sides of the deck or use wood to cover the ends of the siding where it meets the deck.
I hope I did't lose you. Like I said, It's easier to do, than to say.