Do you mean you set all the tools to a common reference point?
Then measure the distance from the common reference point to your part Z zero plane on each face?
Then put this Z distance into the Z column for the Work Coordinate for that face?
If it is three yeses then I think you are doing it the way I work but just describing it a bit different.
Your comment about how the controller uses the values is correct; it adds whatever is in the Z Work Coordinate to H value for that tool.
A HINT which may save ugly holes in places they should not be and also reduce carbide shrapnel scratching the inside of your machine.
Try to set up your reference locations so they are higher than your part zero plane.
The reason for this is then you enter a negative value in the WCS Z.
When entering this Z value it is possible to make a mistake and reverse the sign. For instance you may accidently enter a positive value when it should be negative. That is fine...the tool simply ends up 2 x this value above where it should be and you merrily machine away a bunch of air.
If your value should be positive and you enter a negative by mistake the tool ends up 2 x this value below where it should be. When doing this it probably contacts something a lot more solid than air and you are not at all merry.