Making PLINK compatible files from VCF file without phenotype information
You can use --pheno to specify a phenotype file you want to use, the 1st and 2nd columns being FID and IID. These are just used on the fly and cannot be written to the BED files as I understand. --make-pheno is used to write binary phenotypes, which is unsuitable if your phenotype is actually continuous.
But I still do not quite understand what you want to do here.