(Disclaimer: Don't own the sharpmaker, I just hang out in the maintenace forum way too much lately.)
For the clogged up stones barkeepers friend like someone else posted as well as comet and other things like that will help remove the embedded swarf and glaze. Barkeepers friend being the best. If it's not that bad some dish soap and a toothbrush or something of that nature should help for regular maintenance on keeping it clean. I normally keep a clean shop towel near me to wipe off the swarf on my DMT's with it after every minute or so of sharpening to keep the swarf buildup down and that trick should also carry over to the diamond rods and possibly the ceramics (never used a ceramic).
Use a sharpie on the bevel to make sure your hitting the bevel if your not already doing so. If it doesn't hit it completely you can either reprofile the knife which may take awhile or prop up the sharpmaker on one side side if the presets don't work for you or adjust the angle of the knife in your hand.
Keep in mind that the higher grit stones don't actually make the knife sharper but they refine the edge more. Your goal should be to make an acute apexed edge that is burr free to get a sharp knife. When it is left a coarser grit it is toothy and imagine it acting like micro serrations or saw teeth and they work better for slicing motions. A more refined or polished edge which uses the higher grit stones don't have as pronounce micro serrations if you will and is smoother and will work better for push cutting motions. Both have their uses and neither is better than the other find out what works for you.
Just a little tip you should be able to shave arm hair off their coarsest grit, if your not your either not done or need to improve your technique. If you haven't practiced with it yet try doing so and see how far your technique improves and how sharp you can get your knives as you may surprise yourself as there is a learning curve to everything. I find kitchen paring knives to be perfect candidates due to being thin, cheap, and you typically have several on hand your willing to use or can buy locally for quite cheap.
From my understanding even the diamond rods can be a bit slow for reprofiling so if you feel the need to get that done quicker there is always free hand or a guided setup you can use to speed things up. I personally own the DMT Aligner and found using the clamp from it combined with a cheap Norton Economy Stone (silicon carbide, crystolon) which set you back $10-15 for the clamp and another $6 for the stone can help you reprofile your knives very quickly and should be able to do the majority of the work before switching over to the Sharpmaker. Though it does take some skill to do I find it to be quite a bit more faster than using the small diamond stones included with the aligner. The downside is with that particular stone you have to flatten it typically when you first get it and use something like an old mouse pad or drawel liner to help secure it in place would be highly recommended.
Though I have to side with everyone else the diamond rods are far more useful than the UF, get those first. After that I would recommend a 10x jewelers loupe and pair that up with the sharpie and a good light source so you can more easily see if your fully apexing the edge and where you need improvements, etc. I just spend $10 on a triplet 10x loupe which works decently well and has allowed me to get my knives sharper and put a better edge on it one of the first times using it as I can more easily see what I am doing. Is it OCD, just a tad but so is investing this type of money into sharpening by most peoples standards so you mine as well take it to the extreme and make the best of it.