You can manager preference in two approaches.
1. export/import preferences
1.1 setting preferences in eclipse
1.2 export preferences
1.3 import preferences

2.using -pluginCustomization arguments

2.1 Find the \configuration\config.ini file. open it, and find the id for the
active product(eclipse.product).
For Eclipse the entry will be eclipse.product=org.eclipse.platform.ide. Note
that the active product could also
be defined using an invocation parameter. (-product productId)
2.2 Find the branding plug-in for the product. The product value is the
concatenation of a plug-in id and
an extension id from that plug-in. Look in the \plugins directory for a plug-
in with an id similar to the
product id and see if you can find a file named plugin_customization.ini.
Feature can alos have a branding plug-in. For Eclipse and many Eclipse-base
products the ids are the same,
but the feature.xml file for the product’s feature could be identifying an
alternate branding plug-in using
the plugin=”another.plugin.id.value” attribute for the element.
2.3 Copy the plugin_customization.ini file to a private location, maybe even
your eclipse root directory.
2.4 Add or modify the plugin_customization.ini file content to suite your
needs.
2.5 Invoke Eclipse with the approprocate parameter to have your file used at
runtime:

eclipse -pluginCustomization file_reference

from The Java Developer’s Guide to ECLIPSE