Technically you can use ANY spot color so long flexi sees it as a spot color.
Once you have substituted all your colors to spot using Select By Attributes/Fills & Strokes you need to make sure you have "Spot Color Mapping" enabled within the Production Manger Setup defaults as well as confirming the setting in the Rip and Print.
If you are not using the Gerber colors within your job then you may have to map the spot colors manually. To do this click on the button called "Map Colors" in the Rip and Print Advanced tab. Then select the color you need to map and use the drop down menu to select the color you want.
Then go to the Driver Options and make sure the Process Colors are not enabled.
Then arrange your colors in the order you want. Top colors print first.
Note: If any object fill properties has "Overprint" enabled then this object will print 100% its shape. This is how you layer colors for cool effects. It's also how you scrap a job if you are not paying attention.