There is no real recommendation, but this is how I use it:
\design\<siteaccess>\templates is treated as a default override for the admin/base/standard templates and page-layout stuff. For example, in collaborative sites with lots (main) editing being done on the user side, I would override the general edit templates also there.
And then for class/node/subtree/section specific things, use the \design\<siteaccess>\override\templates as these have priority above all default and the above locations
Templates with no overriderules in override.ini(append.php) goes in: design/<design>/templates/*
Templates which have overriderules in override.ini(append.php) goes in: design/<design>/override/templates/*
Please note that <siteaccess> != <design>. When you do a normal installation of eZ publish it is, but it does not have to be that way. The design for a siteaccess is specified in settings/siteaccess/<siteaccess>/site.ini.append.php