I believe you'll need to look at vacuuming your databases.
PostgreSQL (on which EnterpriseDB is based) has a feature called autovaccuum, which will periodically perform a background vacuum. This releases rows which were previously deleted, for re-use. However, you still need to perform full vacuums periodically. A full vacuum is equivalent to a disk defrag. Deleted rows are removed and wasted space is recovered.
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The base directory is the main place that contains your data for tables/indexes etc. The base directory contains per database directories (named on pg_database.oid). So, the directory titled 1 belongs to template1 and there is another directory for template0. Rest of the directories map to the oids of the databases that you create. Inside each of these directories, you would find different files (named on the pg_class.relfilenode) corresponding to the tables/indexes within that database. For more details and a timely response, you can register on the EnterpriseDB website and post your queries on the forums under the Support tab.