Setting G54 Z zero, work zero set question

We have a haas vf-9 it has a renishaw ts27r tool probe, I was not there when probe was installed, and other cnc guy got fired so its just me, anyways I have used a probe on other machines, and the way that worked was, set all tool lengths with probe, then touch tool 1 to work and input that as G54 Z, on this machine I probed the tool lengths, then I touched tool 1 to my work surface and stored that in G54 Z, but it was not correct and my tool was about 6 inches above my work, does it have something to do with the tool probe macro and the way it saves the tool data?? Right now I am just touching all tools to work with a piece of paper, and have Z home 0 set in G54 Z and it works fine, but I would like to use the probe, I hope this makes sense, and thanks in advance for any help!!

I ASSume you also have the spindle/work probe. You will notice that it is a little less than 6 inches long.
So when you use the table probe to set tools, you will need to set work height with the spindle probe..or subtract the spindle probe height.
Mine is -5.8 in the tool registry.
Gary

Gary thanks for the reply, the next day my batteries for the spindle probe came in, and you were right on target, when I probed Z surface, all the tool lengths were correct, up until this point I had never used a spindle probe only a tool probe, so I didn't realize that it had aot to do with picking up work locations, so everything is working fine now.