Hi
1 -yes
look at the folders and files structure you are uploading, there will mostly already be similarly named folders branching off the \store folder in your case so all you do is upload the lot inside \catalogue into \store

A month or so back someone else asked similar, go back through the thread here

RE. 2... applying sql is done inside zencart, there is a page in admin for it
DO take a database backup BEFORE applying the book sql, just in case of accidents
What sql patch for book does, is add extra tables to the database plus other specific entries.

There is a 3rd party zencart add on for doing complete database backup, you'll have to search for it
OR you can get 'phpmyadmin' OR you can usually do a db backup from your cpanel, using phpmyadmin -assuming its a linux webserver.

The best way to get more info is to trawl the zencart site or forum, for general info, just try to get similar posts about similar things related to what you are doing

Maybe have a practice test site, rather than possibly mess up your special one :)
Most of us learn by practice