So I am trying to setup Mach3 and have some questions.

Is this correct or "normal"? I'm thinking it's not.

On my machine the zero's are
1) Z zero is at the top and increments to the negative while going down.
2) Y zero is with the table all the way forward and increments to the positive while moving to the back.
3) X zero is with the table all the way to the left and increments to the positive when the table moves to the right.

When you home your Mill...where is the table and head oriented?