Well, it depends upon how they are located in the gene map, if they are very close then it's difficult but possible if they are 10-20kb apart from each other. Otherwise you might get a band of 2 genes together. If they are 10-20kb apart then you can just mix 3 primers F+R to make a primer master mix and put 6ul each reaction of the colony. Choose a close by annealing temp for all 3 primers should work. For example, primer 1-56C, primer2-62 and primer 3- 57. So, I would set up Tm at 57C. Again it will be less complicated and crisp if you set up 3 different reaction for different genes.