These two papers, one of which is co-authored by folks here at the DRSC, describe using germline expression of Cas9 for CRISPR genome engineering approaches.
Sebo ZL, Lee HB, Peng Y, Guo Y. A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly (Austin). 2013 Oct 18;8(1). PMID: 24141137.
Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J, Perrimon N, Ni JQ. Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci U S A. 2013 Nov 4. PMID: 24191015. Note: This paper includes a description of our searchable online resource of pre-computed CRISPR sgRNA designs.