Yes. The delivery of the CRISPR-Cas9 ribonucleoprotein (RNP) complexes with Alt-R Cas9 nickases is similar to RNP with the standard Alt-R S.p. Cas9 Nuclease 3NLS, so the same protocol can be used with these enzymes. However, with the Cas9 nickases, two crRNAs are required to generate a double-strand break, while only one crRNA is required for the standard nuclease.
When preparing materials to deliver two crRNAs simultaneously, first prepare RNPs with each crRNA separately before RNP delivery. This will help prevent undesireable hybridization between RNAs.