Ok if you send the machine home for power off before you turn it off then it should be lined up at the cold start marks when you turn it back on. And yes you have to cold start every time you turn the machine on, it won't do anything until that is done.
If you want to set a new home position jog the x and y where you want it then type setho at the command line. I've never moved the z so I am not sure if that would screw with the tool change or not.
You put your fixture offset in the offset page. If you go to where you can put in the tool offsets and press the space bar it will change to the fixture offsets page. Not sure how you have your programs set up but where I work we have tool setters to measure the tool lengths and put that in the tool offsets. Your fixture offset will come from your origin set in your program.
Hope this helps if not or if something is not clear I will try to explain better.