I think we may be talking different things here, you seem to be talking about your hardware limits and me Software Limits.
If you are getting a message saying Softlimits are triggered and you do not have Softlimits set up then you need to make sure you dont have them switched on, button is below the DROs to the right.
If you want to set them up then if your home switches are in the usual position it will be
X , Y Min and Z Max set to zero
X,Y Max and Z Min set to the travels of the respective axis, remebering the Z will be a negative value.
Hood