How the B-engine and the base engine communicate is up to you. I personally like to use an intermediate csv file, which is accessible via the web, and which allows for easy transfer of ideas to the base engine.
The base engine then begins to play a game. In a game, the base engine will use the ideas from the csv file. It may or may not decide to play one of the ideas. If it does play one of the ideas, it will look up the hash table, if the hash table is there, and if it is, it will look if the hash table contains an entry corresponding to the move played. If it does, the base engine will take the move played and combine it with the hash table value. The result will be an idea that the base engine can use to evaluate the move played.
If the base engine finds a result, it will save all moves from the search to a csv file. (The search engine can choose what to save, e.g. only the best moves, all moves, or simply the ones leading to the best result.)
The base engine will look at the csv file and store the hash table with all ideas in it. (Ideas as in the shape of a position with a given score and an idea how to convert a position into a score. The base engine also saves the hash table in a database, but the csv file is the source of all ideas. )
When it runs out of ideas, the base engine will check whether it has access to a suitable opening book. If not, it will check the internet for free opening books. If a suitable book is found, it will enter the opening into the database, using as many variations as possible.
The best advice I can give you is to experiment. Think it through, and make sure you understand how it works and what you can do with it. If you like it and you find that it suits you, you can buy a license. I am personally looking forward to see more chess engines (especially new ones) that work together in this way.
Chess engines are not the only things that can be analysed interactively from the GUI. The GUI gives you the opportunity to compute a lot of statistics, and you even get some nice graphs on top of the GUI. There are some more statistics on a per-game basis available in chessgames.net.