Do I need to dig the rocks out of the soil? And should I use new soil?

There is a plot behind my apartment, and as I dig it just gets rockier. There are large ones and also small ones that are getting compacted with the soil the deeper I go. I have to dig deep for one of my tomato plants b/c the instructions say to bury 80% of the plant and it is already a foot tall (Roma). I also have a Better Boy Tomato plant but it is much shorter so I do not have to dig as deep. The other two plants I got are Cantaloupe and Orange Sweet Bell Pepper. My area has shale as the bedrock and I am seeing lots of fragments in the soil, as well as smooth river rocks in varying sizes (from huge to pebble) which a past tenant must've used as their choice in landscaping. I live in Northeast PA. The plants are the type that you stick them in the ground along with their biodegradable pot (so the soil they are currently in goes along with them). So do I need to be very thorough in removing rocks/pebbles? And should I use new soil when burying the pot instead of the pebbly stuff?