Figure out some way to circulate the cleaner, no matter what you choose to use. Just letting it sit there will do little if any good. Either assemble the complete cooling system and use the water pump to move it at normal engine operating temperature (best choice) or rig some sort of pump if you're going to clean only the block. If you dilute the muriatic acid as I suggested, about 4 ounces per gallon of water, fumes won't be a problem.
Jerry