How to organize a development environment using Oracle XE 11g?
Any serious development project involves source control and a deploy process - SCM (Software Configuration Management). Make sure you put all your database objects (table, index, packages etc..) under revision control. Put your APEX export-files under revision control. Tag them together with the ddl. This way you have a consistent point in time representation of your "system". Make use of the "continous integration" paradigm - build early - build often. Jenkins CI will be a good choice.

When all of this is in place, you branch off your "serious customization"!