I don't have it yet, but have read the manual...
Nice manual, eh?

I wrote it!
1. If I am only making 2 cups in the morning and 2 cups in the late afternoon, would I leave the machine in position 1 all day and position 2 when preparing to make shots ? or just position 2 all the time so its ready.
There is no reason to leave it in position "1." That just runs the pump to be sure that the boiler is filled before turning to position 2 which engages the heating element's activity. A one hour warm up is sufficient, but don't be surprised if you begin drinking more coffee.
2. "Cooling Flush" the Grouphead pressure to stabilize the temperature is a new concept to me, so if I understand right, that you need to relieve the pressure for a few seconds which will bring down the temperature to shot temperature ? Is this right ?
As the machine idles the water in the heat exchanger overheats. The flush is the get that out of the heat exchanger and to stabilize the brewhead temperature. Eric's adaptor for the E-61 is an excellent addition to any E-61 HX machine. it allow you to flush to a specific temperature every time. The flush only needs to be done at the beginning of each session after the machine has been sitting idle
3. That they recommend leaving the portafilter in its position empty when not in use... I thought this would "Use up" the flexibility in the Gasket faster having constant pressure on the gasket ?
leave it in the brewhead, but do not tighten it all the way. The heat will harden teh gasket long before compression will damage it.
4. To put the empty portafilter back and shoot a shot thru it to clean the portafilter. I had just been running it under the tap to clean it.
You can run water from the brewhead into the PF to clean it, but not while it is locked in place. That just swishes the old grounds around.
I hope the Mazzer and Domobar will make that 20 second honey flow appear. Its been years with lots of machines and I have not had that yet. I have had some great coffee, but not the "honey flow"
if it doesn't then the problem is either you or the coffee..

For cleaning: Urnex Cafiza for backflushing. Urnex Dezcal for descaling are my favorites.