I tend to place the strategically to let out the most air and use a fork with one of the tines bent down.
None of my loaves have been used in a liturgy yet, so just practice. IDK, what prayers are to be used when making the holes or what symbolism there is. I don't see anything in my prayer book. I'd probably just use the morning prayers since they are pretty standard.
Fr. George (from prosphora.org) said that if you are the type who prays when they do something, then pray when making prosphora. If not, don't force it. For me I just say a short prayer that the prosphoras would come out nice, worthy to be offered on the altar.
As for the 5 holes, a friend commented about the 5 wounds of Christ (the wounds he retained after the Resurrection). But for me it depends on the size of the prosphora I will make. The bigger, the more holes I will poke.