By default, all configuration files should be put in a folder named ".constellation", in the home folder of the user which launch the server.
if you want to use a custom folder goes to section 1.2.2. JNDI Resources
Labels
Page: 1.2.1.1. PostGRID
Page: 1.2.1.2. CSW
Page: 1.2.1.3. SOS
Page: 1.2.1.4 PostGIS
Page: 1.2.1.5 Shapefiles
Page: 1.2.1.6 SLD
Page: 1.2.1.7 WMS Portrayal Service
Page: 1.2.1.8 Mosaic
Page: 1.2.1.9 Generic File