Pre Setter Machine Coordinates

I had a Renishaw pre setter installed in a Haas VF4. When it measures the tools, it place the actual length of the tool (Distance from machine zero (Table top) to the gage line), in the tool length comp register (Like if you were to measure the tool with a height gage). My part zero is on top of the 4th axis trunnion table. All of the other tools that I use, that are not endmills get measured off of a 2" gage block from the trunnion table and have a negative tool length(I'm guessing this is from machine reference Zero to the touch off point). These tools have to be measured from the trunnion for now. I'm a little lost for now on how to offset these tools that are measured from the pre setter. I would think I should just be able to probe the distance between the table and trunnion table and offset the tools this distance in my program. Am I thinking the right way.

You're overthinking it.
Touch off all your tools with the probe and then bring down one of the tools to be used in the program and touch it off on the trunnion table and set that as your G54 Z0 (or whatever work offset you programmed it as). That's all there is to it.