I always make sure that the issue isn't being caused by bad or dirty maintenance parts. I clean everything really well and then replace parts if needed. Once I know that everything should be working properly and the clog persists, I move on to soaking. Normally I just use forceps to clamp off the cap top tubes being very careful not to clamp too hard. Then fill the caps with cleaning solution until it has a nice bubble above the edge of the cap top. Then I park the heads on the cap tops and leave them there for an hour at most. I also unplug the machine when I do this to avoid surprise cleaning cycles. I generally use a harsher solvent than what comes with the machine for this and the Bordeaux brand flushing solution has been working the best for me lately. When it's done, I unclasp the tubes and run a strong cleaning cycle. This hopefully will break free most of the clog. If I saw no improvement at all, I move on to flushing. If I see a little improvement I might do another soak but rarely as I don't usually get better results.
The proper way to flush a head is to hook a syringe to a new damper, then hook the damper to the head as normal. You push the solution through the damper and into the head. I prefer to lose the damper and hook the syringe directly up to the head using a soft tube. The I push very lightly until I see the solution bubbling out of the nozzles. I let it sit for about a minute so it can break up all of the dry ink inside and then push more through. I do this twice usually and then I push just hard enough to see solution spraying out of the nozzles. You can actually see which nozzles are missing when this happens. I don't ever push any harder than that and just let the solution flow until I see the nozzles recover. If they don't I replace the head. Keep in mind that depending on the age of the head and the ink you use, you will be successful about 50% of the time. The older the head, the harder it is to recover. Sometimes nozzles are just damaged beyond repair. Sometimes the piezo crystal has failed and that is impossible to fix. Sometimes the membrane between channels is broken.