Finding differentially expressed genes between two samples
If I understand your question correctly, you can simply use SetIdent() to change the "default identity" to your samples and then use FindMarker() with the ident.1 = "Double-KO" and ident.2 = "Shox2-KO".

Alternatively, you can "collapse" or "summarize" your single cell data into a pseudo-bulk and then use one of the bulk RNA-seq packages.