the tallest leaf is a starting to brown and has some holes in it...should i trim this leaf back?...should i just place the rock on top of the gravel?...i have it buried at the moment.?
Do not trim the leaf for now. Place the rock on the gravel -- do not bury it.
it might be a good idea to bury it if you don't want it to be seen.
I'd trim off the entire leaf if I were you.
Well, no one ever said that eeryone on this forum is in agreement.
Let me add to your confusion.
I have java fern growing fairly rampantly in my aquarium, two varieties. I bought a book and looked for care advice on the web when I put them in, and never saw anyone suggest burying the roots. In nature, java fern attaches itself to things -- rocks, logs, the ground -- and grows very well that way. The farther it is from an object, the longer the roots will grow. I have a large driftwood type decoration and another small one, and the ferns are all attached to those. I looked for a likely spot, then attached them temporarily by setting a small rock on the roots to hold them there until they grabbed on. I've seen where people use rubber bands, too.
As for the brown leaf, it is the tallest and thus probably the oldest leaf. Leaves die. Leaving it there doesn't help the plant like with tulips. It just sucks energy from it and makes it take longer to form new leaves. I'd prune it. Pruning stimulates growth.
Btw, once it starts growing little java ferns (and mine does this without any leaves turning brown) at the tops of the leaves, I have read that it is best to let them detach from the plant on their own and then find them a spot or give them away.
My two cents. Good luck.