Photos are in order below.
For genetic crosses of any type, control of the genotypes of the crosses is very important. What I usually do is empty the vials in the morning then check the vials at lunch time and then again before going home for the day. Any flies that emerge from the pupa during this time will be good to use in a cross. Slow the flies down by cooling them in the fridge and then keep them immobile using icepacks under a petri dish. Make sure you tip the vial on its side or upside down so flies will not get stuck in the media.