Firstly, you only need qPCR if you are trying to determine the copy number compared to a single copy chromosomal gene, regular PCR would be good enough for presence/absence detection. I would recommend checking GenBank for the sequence of your genes. Primer Blast can do some automatic primer design but if that yields no good options you can always do it manually and then use the Multiple Primer Analyzer tool on the ThermoFisher Scientific website to check for problems.

Ex-Ex Primer can be used to design primers.

http://resource2.ibab.ac.in/exprimer/