The 3-in-1, is that the one with the interupted diamond surface and little ceramic crock sticks? If it is, avoid using the pull through section.
How long is the blade you are sharpening and is it flexible? If I had to guess, the heel("back") is getting sharp first because that's where the blade is most stiff. As you get towards the belly(curved part) and the tip, the pressure you are putting on it is changing with the flex of the blade. Try focusing on one side at a time on just the diamond surface using LIGHT pressure. Work the one side until you are confident you have a good stroke going on. Sharpen the first side until you feel a burr form on the other side of the edge. There is plenty of info on Bladeforums about burrs, use the search function and read away. Once you have a burr established on the entire edge, flip it over and do the same to the other side. The second side usually comes up quicker(forms a burr) unless your edge is really messed up.
This is when you switch to the ceramic rods. Start with the round side as it's more forgiving to an imperfect technique. One side then the other or alternating strokes, it doesn't really matter at this point because you are refining an already sharp edge. Just try and be concentrate on your form(keep the blade straight up and down like you are trying to scrape something off the surface of the rod.). Remember, freehand sharpening is a slow process when you are a beginner. Take your time. Stop periodically and clean the stones with scouring powder and a green scotchbrite.