Some will naturally be CGI, it has to be because we simply don't have the means to have hundreds of B17's etc flying about getting shot up haha.
But for the film, real P51's were used alot, they were painted up to represent the authentic squadrons and flown to Prague i believe.
Here's a clip -
Watch from 53 seconds and also watch from 1:23, wow
Personally i cant wait for this film, i need a break from the chick flicks the Mrs makes me see.