Configuring J-Ben is done through the Preferences editor. Currently, you can configure the kanji dictionary, the display fonts, and J-Ben's mobile/standard mode.
Most configuration options have to do with the various data contained within KANJIDIC. KANJIDIC has tons of information, and much of it is overkill for the purpose of most students. A set of fairly sane defaults are chosen, but you can modify these as necessary. Most options are self-explanatory.
If you own a paper kanji dictionary, or a set of kanji flash cards, you may want to check through the dictionary reference codes. Index codes for many dictionaries and several flash card sets are included. For example, I personally use the Kodansha Kanji Learner's Dictionary by Jack Halpern, so I usually have this code enabled so I can very easily reference it if I'm not satisfied with the output of KANJIDIC.
If you set up a vocab study list, then there's a useful option to display words in your vocab list which use the kanji you're looking up. This option is strongly recommended. If there's nothing in your study list, or nothing that matches your search, then this option doesn't display any extra information.
The "other information" option is for the various other "excessive" data contained in KANJIDIC but which I feel most Japanese learners usually will not need. This includes JIS and Unicode hex codes, various radical index numbers, Korean and "Pinyin" romanizations, dictionary cross-reference codes, and any other KANJIDIC fields not handled elsewhere.
Finally, if you install one or more of the KanjiCafe.com stroke order diagram packs, you can toggle whether to show them here.