I received several fossils and stones but once I returned to the above world I could not figure out how 2 use them, could not even find them.
You can, of course. Here's how:
Hope This Helped :D
You have to open up the menu and press "Send to top" or something similar to those words (i haven't played platinum in a year) and then they will show up in your bag and not in your underground thingamabob. Source: i have played platinum before and this is what i did.