I use the DMT Aligner to reprofile the blade than I free hand sharpen using the stones. I just move the blade as far out of the clamp as I can while it can still securely hold it so I can reprofile those traditional blades as they tend to be a bit narrow. If I wanted to use the Aligner for sharpening purposes as well I would have to come up with a good space system (coin, measured length, etc) so I could keep the blade in the same place between sharpenings and probably make a small set of notes on each knife on placement and angle for reference.
Unfortunately if you have the blade moved all the way in the back of the clamp with the smaller blades it's quite possible you have the entire blade in there, or you might start grinding away the clamp and not the blade which happened to me the first time I used it.
But in all honesty I think freehand is probably the way to go, it just seems like you have to jump through some hoops to get those smaller blades to work right in most sharpening systems.