During your initial set up, the height of the head is the most important decision IMO. If you want the maximum distance from the mill spindle from the lathe spindle you would want the head of the mill parallel to the ways of the lathe.
Now if you want to repeat the alignment of the mill head relative to the rest of the machine here is what you can do:
First make sure your machine is level, which you always want anyway.
Securely attach a laser pointer, even a cheap one, to the mill head and point the beam of the laser horizontally at the wall across your shop. The further from the machine the better.
On the wall where the dot of the laser hits draw a vertical line on the wall.
With this method you can the return the mill head to the same position, even after moving the head up or down.
If you do this carefully, it is pretty darn accurate. You can do this with any round column mill or drill press.
I hope I have made myself clear! Dave