Boxtool is a perl script that lets you work with blocks, boxes, site controls, and special pages in your favourite text editor instead of through the web interface. It is found in Scoop's scripts/ directory. For any of those, but especially the longer items, this allows you to take advantage of your text editor's features like syntax hilighting and text searching, and makes changing them much easier.
Changing the database directly, either through the mysql shell or an sql patch, is not recommended on a live site, because Apache must be stopped and started for the changes to be noticed by Scoop's cache. Most of the site-wide data, such as blocks, boxes, and so on are cached in the Apache process to reduce the load on the database. The cache's timestamp is updated when changing any of those items via the web interface, and therefore doesn't require a fresh start for Apache. Directly changing the database does not update the cache's timestamp and leads to a very confusing experience as different Apache processes update their cache at different times; the same page request will get different results depending on which apache process handles it.
Boxtool updates the cache when it saves information to the database, notifying all apache processes to get the new information immediately.
For details on the different options and commands boxtool accepts, run it as `boxtool help' or `boxtool -help'.