I need to use some open source protocols for a piece of P2P software I
am releasing and I need to know what steps I should go through to
insure that I am doing it leagally and within the GNU license of any
other leagality that may apply.

I need a deffinative "yes you can use either protocol" or "no you
can't use either" and if the answer is no some other protocol
suggestions.

Before I did anything even remotely connected with releasing P2P
software, I would read and make sure I understand the recent US
Supreme Court Grokster decision at
http://caselaw.lp.findlaw.com/cgi-bin/getcase.pl?court=US&navby=case&vol=000&invol=04-480

It is not peer to peer system like that... file trading is not it's
primary function, and will also have copyright protections.

OK, that's good.  When you say GNU, do you mean GPL (see
http://www.gnu.org/copyleft/gpl.html)?  "GNU" is an OS (see
http://www.gnu.org/); "GPL" is the open source license under which GNU
is licensed.  Are you sure that all the open source protocols you want
to use are licensed under GPL?  If yes, then I think this is a simple
matter of reading and complying with the GPL license.  Otherwise, what
licenses govern the protocols you want to use?  Are there clickwrap or
browsewrap licenses in place to which you agreed prior to downloading
the kernels?

Sorry... yes I meant GPL. We have just started the development and my
developers are asking me which protocols we can use legally. Gnutella?
Opennap? Any suggestions? You are asking me pretty much the question I
am asking here, which I am not sure of and thus asking :)

Just trying to clarify.  Please understand that I am just a commenter,
and comments are free.  A complete answer to your question, then,
would require either (1)  me or another commenter, for free, to find
and read the licenses (since not all are governed by GPL) associated
with all the open source P2P protocols (presumably this could included
Gnutella, Opennap, Kazaa, Bittorrent, Morpheus, eMule, Freenet and
others) and opine as to which you may use in the commercial
development of a P2P package or (2) a Researcher to do it for $20.00. 
I am pretty sure GPL does contemplate commercial distribution of
products based on that license, as long as you include the complete
source code and permit others to redistribute and create derivative
works.  Not sure about the others.  Maybe someone else will also jump
in here, now that we've clarified the question.