Question about how an application should store "system"

I have decided that I'm going to resume working on my pgDesigner project
( http://www.hardgeus.com/projects/pgdesigner/ ).  I haven't really
maintained it for over a year, but I get about 200 visits a day to the
project homepage, and about two or three emails a week asking for help.
As the project currently stands, it stores datamodel information in a
text file separate from the database.  What I would like to do is modify
the application such that it can operate in "live" mode.  i.e. store all
visual datamodel information in the database itself in a series of
tables.  My question for this list is the following:  Is there a
standard way for storing quasi-system related information in Postgres.
i.e., this is essentially an admin tool, and I was wondering if there
are naming conventions etc. I should follow such as the table names etc.

John