I suck up the crud on the bottom with a turkey baster and squirt it into a quart container. I find that I have way fewer fry to put back in that way. I do it every couple of days, just a quart or two. Also, I leave a glass chimney in the tank and pour the clean water into it. The water seeps out the bottom of the glass into the tank and doesn't disrupt the water or the fry.
A turkey baster is a plastic tube with a rubber bulb at the end; it's made for drizzling butter on a chicken or turkey while it's being roasted in the oven. You squeeze the bulb at the end, stick it in the water, and then slowly release the bulb, and the water gets sucked inside. I use it for sucking out poop and uneaten food in my betta bowls.
You can buy a turkey baster (get the biggest one you can find) in the housewares section of a store, where the kitchen utensils are found.
A glass chimney is the glass "tube" open at both ends that is used in an oil or "hurricane" lamp. Sometimes you can find these where lighting fixtures are sold, with oil lamps and sometimes where candles are sold. Usually they are bigger in the middle and smaller on each end, although sometimes you can find some that are straight.
Glass chimneys are also very good to put the female in when introducing her to the male in the spawning tank. Since it is open on both ends, removing it doesn't disturb the whole tank the way a jar sometimes does.
