JDeveloper provides you with pre-build install of weblogic and a bunch of useful templates for JRF etc. There are time though when you really need to apply a new template. (For example if you are doing Async web services).
This isn't a problem on windows as the domain is easy to find,
$USER_HOME/Application Data/JDeveloper/system.X.X.X.X/DefaultDomain, but on Unix the location is under a "dot" directory,
~/.jdeveloper/system.X.X.X.X/DefaultDomain. This causes a problem for the graphical domain configuration wizard because it wont let you pick a domain that lives in a hidden directory. It also doesn't have a box where you can just type your path which is annoying.
The most obvious workaround is to use the configuration wizard in text only mode which gives you an old fashioned but workable UI. In this interface you can just type the path of the system directory when it asks you where your domains live. Don't fall into the trap I did of giving it the full location of the DefaultDomain, it will prompt you for this on the next page.
If you prefer you can also use wlst for the same work. Just issue a readDomain, then an addTemplate, updateDomain, then a final closeDomain.