The first thing you need to do is remove the outer sleave from the Cat 5e. I usually just do this with a regular box-cutter, cutting away about one inch of the outer shielding. Next, you need to untwist all four pairs of wires, and straighten them the best you can. Arrange the wires into one of the above wiring schemes (B is most common, but A works just as well). You need to grip the wires so that they remain in order, side by side. You'll have to trim off the tips so that they are even straight across, and only about 1/4-inch of colored wire is exposed above the jacket.
Gripping the wires in one hand, now comes the hard part. You need to fit the plastic connector over the wires, making sure that the tab side is facing away from you (assuming you're holding the wires exactly as pictured above). Once you're maneuvered the wires into place, ensure that they reach all the way to the bottom of the connector. To secure the connector, fit it into the slot on the crimping tool and squeeze the handle. This will cause the prongs to puncture the wire insulation and connect with the inner copper.
Repeat this on the other end of your cable. If you do both ends as A or both ends as B, you will create a standard Patch cable. If you do one end as A and the other as B, you will create a crossover cable. Have fun making cables out of the rest of your spool and selling them to friends! I know I did.