Like you, I only have a few right now.
I am catching them and putting them in a holding cage so I can clean. I only have 4 babies right now in a 10gal.. and one pair in a cage.
The ones in the larger cage I just work around. Yes, they don't like it... but neither do the other birds in with them. lol...
I would suggest you try using the pine pellets that has been suggest in various threads.
I switched to them recently, and love them! The 4 babies have gone almost a week with no odor, and it's still pretty clean.. By babies, I mean several weeks old and feathered out.. not tiny ones.
I put grass clippings in one half of the cage for a soft place to lay and they love it.
If you don't want to remove them to clean...I would work slowly around them. They're not happy, but there's not much you can do.. They are flighty by nature. open the top just enough to get your hand in... and cover the rest of the opening with a towel to prevent escapes. That's how I feed and water.
Your best bet is to find a good absorbent bedding so you can clean less often.