Using .htaccess for redirects

I just started manually writing 301 redirects into .htaccess via FTP but I noticed that my iThemes security settings allow the plugin to write to the file automatically.

Will iThemes remove the redirects underneath “# END WordPress” when it writes to the file?

Also, If I edit the file locally, say after a couple of weeks of inactivity, and put it on the server, what will happen if iThemes has modified it and I have overwritten with an older version + some additional redirects?

I’d like to continue modifying .htaccess locally without affecting iThemes updates, please show me how this is possible.