[EP-underground] cfg dyrectory

Hallo,
I've found two cfg directories, one is in /eprints2 root and one is in 
my archive directory.

/opt/eprints2/cfg
/opt/eprints2/archives/abcd01/cfg

So to set the behavior of entire site (header and footer in templates, 
files and module incusion) do I've to work on general dir or in single 
archive dir?

I'm sorry for my verbosity, I inherited this job about setting an eprint 
archive form an other programmer, and now i have few time to finish the 
work and few time to read the manual closely.

Thanks
Alfredo Cosco