The cracks you are seeing are normal and will come with age. If you let them go the cracks will fill with water and eventually work there way down to the roof and create a leak.
Clean the cracks with a good scrub brush and some dish soap. If you want you can also use other products that have been mentioned after the scrubbing, just use them sparingly and try to stay off the rubber part. Make sure the area is dry prior to applying new Dicor.
Working in 1-2 foot sections spread a thin layer of Dicor self leveling over the old (clean) caulk. I like to use the back of a plastic spoon to then smooth it out a little. This makes the leveling occur faster and also gives you some control on where the Dicor goes. I also cut a 2 liter pop bottle in half and lay my caulk gun in it. Otherwise you'll have a mess when you're not running the gun.
A warm sunny day with a breeze is best. You may see some bubbling of the roof where the new Dicor touches it. The longer it takes for Dicor to dry the more bubbling that will occur. This will lay flat in a week or so. Again a thin layer is best, not gobs and try to just stay on top of the old chaulk.
You don't have to remove the old stuff unless it is lifting off the roof. This means that section of sealant is shot and needs to be replaced.