At present, ProFTPD has seven different configuration contexts: "main" server, <Anonymous>, <Directory>, <Global>, <Limit>, <VirtualHost>, and .ftpaccess files. These contexts are checked for in configuration handlers using the CHECK_CONF macro.
Valid Configuration contexts
The "main" server context, listed as "server config" in the configuration directive documentation, encompasses everything outside of the other contexts (i.e. every configuration directive that is not explicitly contained within another configuration context), and signalled by the macro CONF_ROOT in a configuration directive handler.
The <Anonymous> section is used to set up the very common configuration of an anonymous FTP server. It does a chroot() to the anonymous FTP directory by default, and turns off the requirement for a valid password, requesting only a valid email address as the password. Other system binaries or files need not be contained within the <Anonymous> directory.
Note that since an <Anonymous> section is not considered a separate server, but rather a "subset" of its containing server, any configuration directives set for that server will be in effect for the <Anonymous> as well, unless overridden by a directive of the same name in the <Anonymous> context itself.
The <Directory> context is for configurations specific to directories, of course. This includes views of the contained files based on the logged-in user's username or group membership or on the name of the files (e.g. Unix-style "hidden" files), and on whether the user has permission to see the files. .ftpaccess files occur within this context by definition; <Limit> sections often appear in a <Directory> section as well.
The description in the documentation for the <Global> context is good. Another point to know is that if a directive is set in this context, and then the same directive is used in the main or <VirtualHost> contexts with different parameters, those parameters take precedence over the <Global> parameters. This allows you to configure things for everyone equally, then tweak specific servers individually, on a per-server basis.
The <Limit> context is used to place limits on who and how individual FTP commands, or groups of FTP commands, may be used.
These files are akin to Apache's .htaccess files, which are parsed-on-the-fly configuration files -- with restricted scopes -- that users can place in their own directories. Note that .ftpaccess are similar to Apache's .htaccess files, they are not the same. For example, ProFTPD's .ftpaccess files do not support a "require" directive, nor Apache's AuthRealm directive. That particular area of Apache configuration is targetted for restricting access to anonymous connections; by its nature, ProFTPD handles anonymous connections as special cases of the normal authenticated connections.