How you identify flies with the desired genome modification depends on the frequency of the mutation and its molecular nature.
T7 endonuclease I assay
The T7 endo I assay detects small (a few to tens of basepairs) mutations in heterozygous flies.
Direct sequencing
By using optimised tools and protocols CRISPR/Cas genome engineering can be so efficient that it is possible to identify mutants by directly sequencing the target locus of a few randomly selected flies.