Someone once inquired about this before, so this was the reply I sent by pm:
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I just use hot water and a couple drops of dish soap. I also make sure that nothing will rub up against each other if I can, particular nice metal stuff. I also use the plastic tray, as I've read it's best not to have something resting on the metal bottom. Always check for anything small that may have shaken loose, this happens sometimes with post screws or o-rings.
This is the drying mat I use for my attys, just fyi:
Amazon.com: OXO Good Grips Silicone Stemware Drying Mat: Dish Racks: Kitchen & Dining
Nothing special about it, except that there are no holes for things to get lost through and it doesn't take a lot of space and can easily be put away.
Otherwise, don't use you an alcohol soak or anything else acidic or alkaline, because if you forget your attys in their long enough (e.g., overnight) it can erode the chromium oxide layer.
I use the ultrasonic to pretty much clean all my atomizers and wire. Depending on how dirty it is, I may only give it a 3 minute clean or something longer.
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One other thing I'll add since then is that I noticed the center of the tray has finer holes than the outer section, so anything involving tiny screws or parts goes there. I also have a fine screen debris catcher in my sink, not that I bought it for this, but it makes sure nothing goes down the drain.