There's a whole bunch of ways to set your tools. Depends on what you have available to you.
For example, we have an offline tool presetter. There is a standard tool which measures 4" to gage line that we calibrate the presetter to. All tools are set on this machine. All tool lengths are positive. All work offsets for z are the distance from the 0" gage line (basically the face of the spindle)
So if I took a probe or some other tool, and the probe/tool was 13.123" long, you'd touch it to the top of the part and add 13.123" to the absolute z coordinate. Probes make this simple but you accomplish the same thing whether it's an endmill touching the surface of your part.
Other people will leave G54 Z set to 0 and all tool lengths are negative. In that case, you'd look at the machine coordinates and simply type them as you see them. This doesn't work as well if you have multiple parts at different heights on the table with different coordinates, although you can work around that by having an incremental distance measuring the distance between the top of g54 and g55, for example.
There's others who have tool presetters on the table, or set all the tools off a gage block or similar.
There's probably some nuanced methods i haven't thought of.
Have you been making good parts with relative ease of tool setting? then I'd suggest you maybe stick with what you do. It isn't "wrong" if it works. But there might be simpler (to you) methods.
If you are running a milling program and you know the tool is at Z-.250 but you look at the screen and in absolute it says Z-7.632, that's annoying as hell and the parameter I posted should fix that. It is very likely that hitting reset on your control will reset g43, so after hitting reset, the coordinate should go back to how it looks now.
If in the middle of the program with g43 active, you single block it and go into MPG, the absolute coordinate should still show as absolute with cutter comp on. So if you simply wanted to do some "manual milling", you could literally have a bit of code like this:
T1M6
G90G80G40G17
G0G54X0Y0S1000M3
G43H1Z5.
M0(PUT IN MPG AND DO YOUR MANUAL MILLING HERE)
M0
M0
G28G91G0Z0M19
G90
... and the coordinates you see on the screen should all be absolute with G43 cutter comp enabled. so if you went 1" deep it would show that.