The correct way to cite Geneious is as follows:
In your methods section, please cite "Geneious version (the version you are using) (http://www.geneious.com, Kearse et al., 2012)"
And cite the paper below in your reference list:
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Mentjies, P., & Drummond, A. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.Bioinformatics, 28(12), 1647-1649.