cutting speed vs. rapids with tool up

Newbie here setting up G540. I have 4:1 belt and 5 turn per inch lead screws. When I set up max speed in the step conf wizard is that for rapids (in my case not so rapid but that's another issue... )? My jitter is 25,000 so to get below that I need to set max speed to 0.5 in/sec. But if that is for rapids (unloaded) I could go faster (I think) since I am microstepping and only loose a bit of accuracy DURING the move. Want to confirm that the cutting feed rate is set by the gcode and I can push this a bit. I am going to work on reducing the jitter but for this post just want to understand how to properly set this. I think the real answer is I need to hook up the machine and test...

Yes, feed rates for cutting is set in the g-code with the F-word and positioning moves (G0) are at the maximum rate allowed by the configuration settings. (less override settings).