In HFSS, you need not to make them (patch and RIS) to assign them as Perfect Electric Conductor, rather what you should do is to select your patch and RIS and assign them as pec material, you may do so by drawing patch as a 3D figure (accounting for a very small height/thickness of the patch over the substrate) for example: you may draw a cylinder for a circular patch and a box for rectangular patch but with very small thickness.
Then, i think the problem of the intersection of two bounday conditions won't occur.
moreover, it would be help for others to help you if you can upload your design.
Hope it helps.
Regards.