The perlite under the cakes or trays or whatever route you take is just there to help keep moisture up I believe. If the mushrooms started growing down into it, they wouldn't be able to fully develop correctly. You want them to grow upwards into your chamber for best results. The rye berries are a pretty common substrate, I used Wild bird seed as it was cheap and easily available. Popcorn also seems to work really well and is pretty cheap and available too.
Which ever medium gets prepared, put into jars, preasure cooked, then allowed to cool. The jars get inoculated with spores, and then have to sit and colonize. Sometimes colonizing takes a week, sometimes longer, it depends on a few variables. I colonized my jars in an incubator I made from 2 rubber maid totes and a fish tank heater. The bottom tote had a couple inchs of water with the heater keeping it warm, then the top tote was set inside with the lid on and the water keeps the top totes warm. So after the jars are colonized you can either fruit the cakes if you did that method, or you take the colonized jars and spawn them to a bulk substrate(manure,straw, something like that) allow that to colonize and then fruit them.
Hope that answers a few questions at least.