I have a 24 X 48 mill with a safe working area of 22 X 44, what I am trying to do it to start my cuts at 11 inches on the Y axis to make it easier to cut 2 sided files, I would like to set the home at 11 inches on the Y axis but am unsure how to set mach up to do this.
This way i can mark the center of the piece i am cutting and can just flip it over to do the backside.
Any help would be appreciated

If you home then once done jog to where you want the file to start and zero the DROs, that is you just set up a work offset. So  any time you start Mach you then Home then when you ask it to go to zero it will be at the position you had previously set as work offset zero.
Hood

Depending on how you work, you may want to try using a home offset of -11 for the Y axis in Config>Homing/Limits. This should make your Y axis Z0 in machine coordinates be the center of your table.

Well that works for setting it up at zero but will not let me cut on the negative side and smashes the gantry against the limit switch, i just want to start the cut in the center of the y, not move the work farther on my table

You can place the work anywhere you like and have the work offset zero any place you like so I am not sure where you are going wrong especially when you say "that works" but dont say what it is that works.
Hood

What works is it homes in the center of the Y axis but still only cuts to one side, it basically moves my cnc file over 11 inches, i want to the Y to move left and right of the 11 inch mark, not move the work further out on the table

Home then jog to centre and zero the Y DRO, you have just set up a work offset, you can move positive or negative from that zero position.
Hood

Well, i am not very well versed in Mach as you can tell, I can't get it right. It just keeps on moving my work farther out on the table.
Guess I will keep doing it the long way.

Sounds like maybe you need to have the origin (0,0) of you part in the center of the part instead of at the corner ? If the part is symmetrical on both sides, flipping it in place should do as you want, maintaining the same zero point.
Just guessing,
Russ