There are two levels of configuration: configuring and resaving the image, thereby creating a new image that is exactly as you want it at startup, and configuring certain aspects of LispWorks as it starts up.
These two levels are available for good reason: while some configuration details may be of use to all LispWorks users on your site (for instance, having a particular library built in to the image where before it was only load-on-demand) others may be a matter of personal preference (for instance how many editor windows are allowed on-screen, or the colors of tool windows).
In the first case, you use edited copies of files in the
folder to achieve your aims.
In the second case, you make entries in your initialization file. This is a file read every time LispWorks starts up, and it can contain any valid Common Lisp code. (Most of the configurable settings in LispWorks can be controlled from Common Lisp.) Your initialization file can be changed via
Tools > Preferences...
in the LispWorks IDE.
LispWorks Release Notes and Installation Guide - 23 Dec 2011