The two Marraffini Lab CRISPR Plasmids for bactera genome editing have a spacer cloning site, just wondering why you need two spacers. Do you know if there is a plasmid that can express both Cas9 and gRNA?
I think, they provide the second plasmid only for doing targeting in parallel, e.g. multiple locus at the same time. The first plamid (pCas9) does express Cas9 plus tracrRNA and crRNA already (the natural version of gRNA, gRNA is a synthetic chimeric RNA of tracrRNA+crRNA), if I interpret the figures correctly. The second plasmid only provides more crRNAs for multiple targeting. Other possibility: the Cas9 decribed there is a Cas9 Nickase, so you have to use 2 gRNAs or 1 tracRNA + 2 crRNAs to target sites.