keep the gummi off the base if possible. it will mar the surface. I'd not be afraid to take more passes than shoal007 suggests, as long as you taper your work; don't just work the location of the rust or it will become depressed, relative to the rest of the edge. Work into and out of the affected area. I certainly agree to go lightly with the pressure. Heavy pressure with any edge tool generally results in rolling the tool and modifying the edge angle.
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(scroll down and look for topics on the right). It pays, in the long run, to purchase quality tools, especially files. Ski edges are high quality steel and require sharp, quality tools to work them. Your garden variety hardware store mill-bastard file isn't going to last as long or do as good a job as a fine tool such as a BLU-DAN.
Edge angle guides are also invaluable. This is where you have to make decisions that will commit you to maintaining certain edge angles. A 1 degree base and a 2 degree side bevel are pretty common and a good place to begin. You'll find plenty of discussions on this site as to what other angles you might want to consider. You use the guides with your files, diamond stones and ceramic stones. Gummis you just use by hand.
A light weight set of gloves will save your hands while tuning. Both filings and sharp edges can cause injury. I've seen guys that have severed tendons on uber-sharp race skis. More common are scrapes and small cuts, but better protected than not. Some guys tape their fingers in lieu of or in addition to gloves.
Tuning can be fun and adds a new dimension to your skiing and riding. A smooth edge is faster and more predictable than a burred or gouged one. Enjoy!