Remove the impeller, if it’s in the way. Circulate with an external electric pump and the solvent in a bucket. I use a submersible 110v pump, but many use a 12v and some plumbing.
I also circulate backwards in the circuit, by entering at the exhaust elbow hose and exit at the water pump. Personally, I don’t remove the impeller, as there is nothing to descale in the pump or the other side of it, so I exit via the hose end before it.
The engine does not need to be running at all. If the motor is raw water cooled, pulling the thermostats is typically necessary.
KInda complicated... my RW pump has PITA copper pipes so removing them is not happening. If I do this I would do it like filing the RW circuit w/ antifreeze... but let the effluent flow into a bucket which as the descaler. But that means removing the 2" hose from the elbo and that ain't happenin.... But my engine is freshwater cooled... ie antifreeze circulates in the block... Does that need to be de scaled?
The antifreeze (coolant) passages need to be cleaned too, every so often. The coolant has corrosion inhibitors, so it pretty tame. You drain, then fill with a coolant flush and start the engine to circulate, then drain and replace.
When figuring out how to enter and exit the raw water circuit, keep in mind, you only need to cover the metal passages, specifically the heat exchanger and anything similar (oil collier, intercooler, transmission cooler, etc).
If I felt my cooling system needed cleaning, I believe muriatic acid or MaryKate On & Off Hull cleaner would do the same job for a lot less money. I've used both to clean shell from my air conditioning sea water lines in Charleston, where shell is really bad in the summer.
FWIW, I used diluted CLR to de-scale my HX. I disconnected my raw water pump, then drained my HX through the anode socket and measured how much came out. That's how much CLR solution I put in. I let it sit for about 20 minutes, then pulled it out and pushed it back in again (to mix). Recirculating would be better, but access to all the plumbing would have been very difficult. To put the CLR in, I attached a hose barb to the anode socket and attached a Tygon tube.
I considered de-scaling my freshwater loop, but decided that there's a lot more downside than upside to that. My coolant was due for scheduled replacement, and I wanted to switch to Zerex G05, so I did a flush with distilled water (with the thermostat removed). I did add a bottle of Prestone flushing fluid to the water rinse, but that's more of a neutralizing agent (in case the old coolant built up acid) - its chemistry does not appear to be a de-scaling agent at all. I did some Internet research on this, and it appears that all the consumer-grade acidic flushes were pulled off the market in the early 2000's due to environmental and safety concerns. About the only thing you can find now is Rydlyme, and I wasn't willing to fork over the huge cost for product and shipping.
I am going to run RydLyme through my engine tomorrow. My research pointed toward this product being milder on engine parts. I have a couple of hoses and the raw water impeller pulled, and will run the stuff through backwards. I got a low output fountain pump to circulate. I actually tested my system with water (much higher flow than the RydLyme will be) and had a chunk of impeller blade come out!