The aligner will work with blades up to around 7in or so, small blades like those found on a SAK can be done but your better off just using a small stone or freehand with the diamond's.
First forget about the bevel that is on the knife, you will be completely re-setting it. The factory bevel on most all knives will not even be close to the angles the aligner will produce and for this reason you must grind in the bevel the aligner wants to make. Placement of the clamp has a sweet spot usually just a hair back from half way to the tip.
In this section place a piece of masking tape, this will allow the clamp to better grip the blade. You can also trim off the stop tabs on the clamp because they will get in the way with some knives and allows you more angle adjustment by changing the distance from the edge. With the clamp loose pinch the jaws on the blade, tighten the metal screw to finger nail tight then back off a 1/8 or less turn. You want the clamp the take the angle of the blade sides for best alignment.
After the metal screw is set tighten down the plastic screw until your fingers hurt. Check by trying to wiggle the clamp, if it does not move your good.
For a saber ground endura you would use a level 5 and if its FFG a level 6. Start with your coarse stone (XC would be good to have) and place your index finger on the guide rod using light pressure to hold it down and in one possition. Use your other fingers to support the stone and with just the weight of your fingers as pressure start creating your new bevel.
You can use a zig zag over lapping pattern or single swipes, whatever feels best for you. Work the side evenly and not one all at once. Grind with your coarse stone until you have created a perfect "V" in the blade, as you get closer to this "V" a burr will start to form on the edge. When the edge has been formed the burr will move side to side with each opposing stroke of the stone. Use decreasing amounts of pressure until it feels as though you are not even making contact and this burr will go away.
After the bevel setting process with the coarse DMT your edge will be very toothy and sharp, shaving sharp easily. You continue to process with each finer stone using the same reduction of pressure technique and by the finish of the EEF your edge will be hair splitting sharp.
If the stones are fresh don't expect greatness from the start, they take time to break-in. You will still have a very sharp knife but with time it will only get sharper.
Give her a go and let us know if you have any problems.
