The proper way to do this is to use rhinestone flock to make your transfers. Lay out your pattern as a vector (I like to use lines with a dotted stroke, but YMMV) then cut it on a vinyl cutter and weed out the holes, then put it on a carrier sheet and put your rhinestones in face down. Then you can just put it on the substrate and press.
As far as the flock goes, most HTV suppliers carry a version of it. I’ve used the one from Specialty Materials before and it worked well enough.
And here’s a video on how to apply them:
HMU if you have any issues - it’s been a few years, but I did many thousands of rhinestone transfers back when they were hot.
Also, if you really don’t want to go this route, you can mark your design with a sharpie on the back of a carrier sheet, then flip it over and put down the rhinestones by hand. That’s a PITA and takes forever, but if you’re only doing one it may be quicker than laying out the vector and cutting a proper template.