Can I rename tremded.x86 to somthing different and modify the nohup script to check for it? and ya I know I need to change the net port etc and point it to another server.cfg.
Yes, just make a copy of tremded.x86 with a different name and adjust your second script accordingly.
I would like to have both processes use the same admin.dat but I would like each to have thier own games.log and admin.log. I assume there is a command line switch to define these output files....
Having two servers share the same admin.dat doesn't work very well. The file is only read at the start of each map but is written to whenever !setlevel or !ban is run. This can lead to some data loss. There is also the remote chance that both servers could try updating the file at the same time and corrupt the file. The only way do do this safely is to disable !ban and !setlevel on one of the servers.
You can set the name of each of these files with the cvars:
g_admin "name_of_admin.dat"
g_adminLog "name_of_admin.log"
g_logFile "name_of_games.log"