If you mean that you're trying to use "../thingies" in your .htaccess file, then that isn't necessary. Just leave the .htaccess lines as they are.
If you're using an exec method such as /dh/cgi-system/php5.cgi that Atropos7 mentions above, then that's correct.
Just leave all the cgi-bin stuff in place and only move the .htaccess file to those directories that you want to run under the custom php.ini.
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