With your template for HDR have homology arms either side of your insert that are 50-1000 base pairs long and not recognized by your gRNAs. You can get away with 30-50bp homology arms if you are using a single strand annealing protein system like lambda red or ICP8. For your marker it is probably best to use an antibiotic resistance cassette (KanR is a good choice). The methods in this paper should be helpful (Article Construction of Escherichia coli K-12 in-frame, single-gene ...