Hey Joe,
I've used that wizard and I like it but, I too have questions about doing some of the advanced things (like changing rate). Due to my inexperience with the whole CNC process, I usually just try different workarounds to solve my problems.
So... long story short, My workaround for the same problem you are having is, I used the wizard to generate the basic code and have it kick that back to Mach 3. Then I would used the Edit G-Code button to go in and add the Feed Rate changes that I wanted at the appropriate line. It's pretty easy to do it that way. Perhaps not the most elegant solution, but nobody has ever accused me of being a stylst

Good Luck!
Sid