I have a 4" pvc tube that come straight up through the concrete it is capped off and is stuck in the ground. I am pretty sure this is a stub for a toilet. My question is how do I install the toilet do I need to work the pvc loose or do I cut it off floor level and set the toilet on it? Also there is a stub for the bathtub that is next to it. It is full of white rock can I leave it filled in with this rock or do I need to remove it all first?

For the toilet you need what is called a commode flange. Depending on what kind you get will determine where you need to cut off the PVC sticking up through the concrete. You will then use a bowl wax and closet bolts to anchor the toilet down. Make sure you buy brass bolts.
Now about the tub drain, do you plan to install a bathtub? If so you will have to clear any obstructions in the pipe before you connect the tub waste and overflow.