I would suggest buying a base edge file guide. I have an adjustable one that cost only $35. It has guide bead non-concentrically mounted on the base guide with notches. You rotate it to lift the guide at the appropriate angle.
Another problem you are going to encounter if you simply partially engage the file into the guide, in addition to creating the edge step, is you are going to form a non 90 degree angle. If angle formed by my base and side edge beevels must not be 90 degrees, I would always prefer it to be obtuse rather than acute and no more than 0.5 - 1 degree. The reasons are the edge will tend to chamfer off less quickly (requiring less sharpening) and since I personally detune to ride park features, the chamfer I intetionally induce is strong to blunt strikes against objects.
I'd also strongly recommend you set your base bevel, first. This is angle is critical because it's the one that really affects the ride. The side edge is only beveled to keep it as close to 90 (or slightly more) as possible to the base edge.
The other option you have is to shim the third contact point (on the base edge) with something. Perhaps you could use tape or something of that nature. If you are really into getting a good detailed tune out of your entire board, I'd really recommend picking up a good base and side edge file guide.
Thes ones I use are these:
Side edge: SwixSport.com : SwixProduct / File Holders Edger Pro, edge sharpener
A bit pricy, but the best side edge tool I think you'll find. The bearings in the guide are smooth as butter.
Base Edge: Amazon.com: Base Bevel File Guide SKS Vario Adjustable All Angle: Sports & Outdoors
You can clearly see that bronze "guide" bead as I describe above. This one I chose on a whim over the Swix ones and it works quite well.
I set a 1.5/1.5 base/side on my boards though I have ridden 2.0/2.0 and 1.5/2.0. I'd recommend starting with a 1.0/1.0 if the factory hasn't already set one.