If you are running a second offset, and need all your tools to be a different Z,
just put the difference in the Z register of the fixture offset, E2 or whatever.
It can get stupid confusing with all the different ways people set their Z,
and with a few rare exceptions, most of them are correct, just different.
Just remember, the Z offset in your tool table, and Z offset in your fixture
offset ADD.
Say you touch off your tools, just like you are doing now, on your part/fixture,
a number goes into your tool table. Now if you put a number into your fixture
offset of +1.000, all of your tools will run 1" higher.
Get your head wrapped around it, because the more you understand now,
the easier it will be later, and there are still days that I stand here
scratching my head trying to figure out which way whats going.