The kanji study list is used for storing any kanji characters you are studying. It's used by the kanji dictionary and is required for kanji drilling mode. This list can be added to and sorted based on newspaper frequency, Jouyou grade level, and Japanese Language Proficiency Test (JLPT) level.
Editing the kanji study list is done through the kanji study list editor, which can be reached from the Edit menu. (Edit -> Kanji Study List)
If you don't know where to start on studying kanji, I suggest starting by using the "Add Kanji" buttons on the left side of the editor to add kanji by either Jouyou grade level or JLPT level. Just click the appropriate button, choose a range of grades or levels, click "OK", and those kanji will be added to your list.
Other methods to add kanji include the "By Frequency" button, which adds kanji by newspaper frequency ranking, or the "From File" button which finds the kanji contained within a plain text file. (Note: "From File" currently only works on UTF-8 encoded files.)
The Kanji Study List editor lets you manually edit your kanji list. You can type kanji in by hand, or copy and paste them from another application.
When you hit the Commit button, your changes are saved. Only kanji which are in the kanji dictionary will be retained; any other characters are discarded. Duplicates are also automatically removed. So, you could simply copy and paste a vocab list into the kanji list editor, hit commit, and you would end up with a list of all the kanji used in that list.
After adding characters to the list, it is strongly recommended to sort the list. The editor allows 3 methods of sorting: by newspaper frequency, by Jouyou grade, or by JLPT level. Currently you can only sort in ascending order.
J-Ben uses a "stable" sort for sorting study lists. This allows a nice trick where you can first sort by frequency, then by Jouyou grade (or JLPT level), and the result will be a list sorted by grade but with the characters within each grade sorted by frequency.
The vocab study list can be edited via the "Edit->Vocab Study List" menu item. This study list is primarily used as a cross-referencing resource for the kanji dictionary. The list is formatted with each line representing one Japanese word or phrase. Either manually type in the list, or copy and paste it from another program, and press Apply or OK.