Tagaini's interface can feel a bit dated and the fact it does not try to follow a particular study methodology may also be confusing to new users. Also the manual certainly needs a brush-up.
The key to using Tagaini effectively is to understand it is just a discovery tool and database for your study material - an assistant, not a teacher.
The most important feature is the study list. You can add entries to that list by right-clicking them in the results view, or pressing the blue flag in the detailed view. It is then easy to review and practice them from the "Practice" menu ("whole study list" practice options).
If you are looking for entries in your study list, there is a filter tab ("Study") for this in the search tool. All the filters are additive, so you can make a search for e.g. "all the kanji entries I study which are JLPT N5".
If there is a search you like in particular, you can save it and redo it later in the Saved searches. And if you want to practice a particular search set, the "current set" practice options in the Practice menu will let you do that.
That should cover the basics - make sure to organize your knowledge by tagging it and adding notes. There is also a hierarchical lists feature, but I am not too fond of it personally.
Hope this helps,