If you have any "pest snails" they'll help keep the dead bbs under control.
You can also use fine sponge on airline tubing to avoid sucking up fry for smaller water changes. Also good for when you "jar" them (without the sponge) can syphon most of the waste without running out of water to syphon. I happened to have oxygen tubing that has hard tips, works well if you've got it.