Either way for me, Dee. I have used this method in many cases without having taken the melodica apart. I just submerge it for 2-3 hours, placing something heavier on top to hold it down if necessary. I take it out a few times and work the keys while blowing water out, then re-submerging. Then I rinse by doing the same several times in clear water.
In other cases, I soak the keyboard, reeds, etc. while the melodica is disassembled.
For exotic vintage melodicas that have wooden parts or old gasket material I’m not replacing, or air hole key pads that look fragile, I don’t soak the whole thing. I don’t do it with whole vintage Italians, especially the Clavietta, and I wouldn’t with a Hohner Pro 36.