If you're going to try to "clean" them with a wiper tool, slide the dust seal up and out of the way. A thin screwdriver or butter knife can get under the edge to pry it up. Then get the tool in there to the fork seal and finish up with an airhose to remove any debris. Tap the dust seal back down to complete it.
IMHO, if you are going to replace fork seals, I would highly recommend OEM seals in this instance. I have never had long-term luck with K&L (or any other) fork seals. Get your dust seals from whomever you want (I get OEM here too). I also use a scotch-brite pad very lightly with a little bit of breakcleen on it to polish the tubes to remove any small pock marks - but don't use it so hard that you change the sheen on the tubes, unless you have a bad dig you need to reduce. These little dings carry dirt in and slowly deposit inside the seal lip to start the process all over.
Again, finish up with an airhose.