First things first. You will set the limit switches to active high or active low based on how it is connected to the circuit board in your machine controller and will differ from one machine to the next. For example, one of my 3-axis machines uses one active high and two active low switches. Basically, you will use whichever one works for each axis. In your case you will choose active low, meaning that the switch is providing a ground signal to the PC with the switch has been activated, and the rest of the time it is at +5V.
Now, to your homing problem. The "REF ALL HOME" button is a VB-Script. Here is how to modify it to do your dirty work!
Go to "Operator" > "Edit Button Script"
All of the button with VB-Script attached to it will begin to flash. Click the "REF ALL HOME" button to edit it.
Now that you're in the editor you should see something like this without the comments:
DoButton( 23 ) ' Ref (home) Y Axis
DoButton( 22 ) ' Ref X Axis
DoButton( 24 ) ' Ref Z Axis
DoOEMButton(133) ' Zero X Encoder
DoOEMButton(134) ' Zero X Encoder
DoOEMButton(135) ' Zero X Encoder
Simply change this to read:
DoButton( 23 ) ' Ref (home) Y Axis
DoButton( 22 ) ' Ref X Axis
DoOEMButton(133) ' Zero X Encoder
DoOEMButton(134) ' Zero X Encoder
DoOEMButton(135) ' Zero X Encoder
It will now home Y, then X, then zero X, Y and Z.
Also to note, this script is slightly dated as DoButton() is a deprecated function. To bring it up to date with the times use this script:
DoOEMButton( 1023 ) ' Ref (home) Y Axis
DoOEMButton( 1022 ) ' Ref X Axis
DoOEMButton(133) ' Zero X Encoder
DoOEMButton(134) ' Zero X Encoder
DoOEMButton(135) ' Zero X Encoder