Yes, The only way to set a G1 value is in Gcode or from the MDI line. But, if you load a gcode file and it doesn't have a F value in it before you start the program you can manualy enter a feed rate into the feed rate DRO and it will make any feed moves at that speed.
Fixture save saves your work coordinates. What this does in short is allow you to close Mach and on reopening , once you refrence the machine and hit go to zero it will put you right back at the last used work coordinates. I think the problem you are describeing may be in the way you are saveing/editing your drawings/gcode.