The flies I use are produced in a laboratory and stripped of all fungus and bacteria, so I just place a cup with the appropriate amount of pupated flies in it then push one of those green calcium cubes against the screen to control where the flies fly once they hatch out.
i use a container with a stopper 1/8 the size of my container, i then open the bottom cage door put the opening above the door level and pull the plug till a number i want fly in. the flies routinely flt up ad i have the cage shut before any i rarely loose any