Hmmm. I'm trying to think of how they're typically packaged. Well, if the stems are tied together, untie them ASAP. They aren't meant to be bunched like that. They probably won't fall over. You may have multiple rhizomes in there too.
If you've got some really damaged plants, I'd say cut off the most damaged ones and leave the so-so leaves on the plant. Cut off any soft rotting rhizome parts cleanly. Tie each rhizome to it's own rock, and set where you want. They do grow on top of the substrate just fine, they take nutrients from the water. Then, you just check them periodically to see if any new shoots are growing and how the roots look (warm brown and fuzzy is good; black and fuzzy and squishy is bad)
I hope this helps you. I am not new to plants, but new here. Others may give you different info. This is just IME, and I have bought many many java fern tubes in my day.