So, heres how you would do it.
Flygon @ Power Bracer
Give it ten Protein and battle 31 Patrat/Lillipup. Or just battle 51 Patrat/Lillipup.
Flygon @ Power Anklet
Give it ten Carbos and battle 31 Purrloin. Or just battle 51 Purrloin.
So, it doesnt matter when you EV train it, you just have to do what I put up. Doesnt matter if its level 1 or 100.
Hope I helped!