When talking about the Enterprise Manager directory related structure, there are basically four relevant sections in the Oracle Home, the first one has to do with EMCA, the EMCA directory is where Oracle stores the log files related to EMCA executions, there you will find a directory where generic EMCA output is stored, meanwhile under this directory you will find directories named the same as each Oracle Instance that has been configured by EMCA.
The second section is related to the specific EM console; here there are two main directories, one stores the console configuration, most of these configuration files are not supposed to be manipulated by the DBA unless explicitly directed by Oracle support. There are configuration files that are modified by EMCA.
There is a fourth section located under the Oracle Home named sysman. When a new console is created EMCA reads template configuration files from here and executes the scripts to create or recreate the EM repository...