I've read through the documentation but I still am not sure on how it works or what to do. I read everything about it under the "Backup and Restore" section of Enterprisedb documentation. I have this 64mb files that fill my my directory. Can I just remove the old ones that are more than 3 days old or will this cause the archiving to be corrupt?

EnterpriseDB is layered atop Postgresql. As I understand it, EnterpriseDB uses Slony in at least one of their replication approaches. These files sound like they may be the Slony write history files, which are used to store a complete history of all changes to the database. Depending upon replication subscriber update frequency and history write rate, three days might be fine, but then again, it may not. All replication subscribers must be 'done' with a write history file before you can archive it.

Normally, whenever a complete backup is made, you would start with a fresh set of write history files.