Customization in Pro/E means creating our own config.pro and config.win file.
Config.pro file is used for customization your Pro/E configuration such as your start part/assembly template, unit, number of decimal places and many more. Please go thru the help for config file to see various options available under config file
Config.win file is used to customized your screen appearance such as customisation of toolbars, adding mapkeys to standard toolbar, editing mapkeys grahical representation and many more..
By setting these things at once, you are not required to set all those again and again. When ever you start your Pro/E session, you can get your customized Pro/E environment.
For this it is required to keep your config.pro and config.win file in your Pro/E start directory.
Hope this will help you.
Regards,
Yogesh