If you're not looking for extreme precision, I've had success cutting with the guide rail, without clamping it down at all. If you support your workpiece and rails well (i.e. flat), the rubber strips under the guide rail hold the piece and rail in place really well. I've worked on pieces that are longer than the guide rail, and with some care in aligning the rail to the cutline, I can move the rail along the length and make repeated cuts.
If your workpiece is narrower than the guide rail, I place a second piece of wood of same thickness behind the workpiece, to keep the guide rail flat. If that is the case, you can clamp that support piece down (as a "fence") so that you limit differential movement between the 3 elements (workpiece, support piece and guide rail)
If you're looking for extreme precision, buy a longer guide rail (at least 6" longer than your work piece), or buy the guide rail connectors and a second guide rail (so the sum of the two guide rails is longer than the longest piece you would like to cut). Extend the rail past both ends of the work piece, and clamp from underneath.
The beauty of the guide rail, is that the rubber splinter guard is right on the cut line! Even without clamping the guide rail down, I find I get greater precision out of this system than most other methods of working.