Standard is like a graph, X0Y0 is lower left corner of the paper. If your home switches are at locations other than that position then you can enter a Home Off value in Homing and limits. The value you will enter is equal to the distance your axis is away from the standard machine zero point when you home.
You can of course set things up any way you like and feel comfortable with but it is best to stick with convention in my opinion as it wont cause issues down the road, setting up unconventionally may or may not cause problems but will certainly make things harder if moving to a machine that observes convention.
One last thing is remember that it is the tool position that dictates the XY and Z zeros and not the table movement. On a knee mill it is often confusing for a beginner as they see the table moving left when there is a positive X move and it looks wrong but if they think about the tool in relation to the work they will see it is right.
Oh another "one last thing"
![Grin ;D](https://www.machsupport.com/forum/Smileys/default/grin.gif)
you dont have to have the home position as the point you start your work, you can jog wherever you like on the table and zero the axis, that sets up a work offset, the stanndard being the G54 but there are many more you can stor if you wish.
Hood