The .htaccess files are in the content directories, e.g. DocumentRoot and its subdirectories. You would normally create these file by hand on a per directory basis.
You can create custom error messages by following this doc:
In the past, I have found a good maintenance mode solution to be starting Apache with an alternative config that changes the document root to a maintenance directory. This directory has no index files, but instead serves custom error documents.
The method I have used for starting Apache with an alternative config, is to add a new option to the init.d script like "maint". One could simply specify the -f argument as $OPTIONS in the environment before running # service httpd restart, but I have found it this way for simple apache configs. The maint option in /etc/init.d/httpd might look like:
# See how were called.
case "$1" in
OPTIONS="$OPTIONS -f $MAINTCONFIG
Where $MAINTCONFIG is either coded into the init script (preferred) or set in the environment. Then to go into maintenance, simply:
# service httpd maint
Which would stop apache, then start apache with the maintenance config. Perhaps not the most elegant, but it served its purpose and is expandable to handle maintenance for individual virtual hosts by devising additional config files for each vhost that maintenance mode should apply.