Yes, in Gen V you can still gain EVs at level 100 despite not levelling up any more.
Smogon article - BW EV training
You can see a level 100 Pokemon gain EVs because every 4 EVs you gain in one stat you will be able to see the stat itself go up by one point.
I suggest you read that article since it will explain most things about EV training.
Note: since your Flygon has been used to battle random trainers, it will have EVs all over the place already. If you want to correctly EV train it, you will need to reset its EVs with 6 specific berries (ones which you can buy a random 5 a day from the PKMN breeder on Route 5 in B2W2 and form the florist in Join Avenue if the Florist is at Rank 10). The same goes for any other Pokemon you've battled randomly before specifically EV training them.
However, there is a simpler and more understandable guide on this website: EV training, which will be a good starting point before you go onto the Smogon article.