If you want to change settings / options based on the filetype there are a couple of ways you can do it.
Using an Autocommand
augroup indent_settings au! au BufEnter *.pl setl autoindent smartindent au BufEnter *.html setl noautoindent nosmartindent augroup END
The above will do a setlocal when entering a perl or html file. It will turn autoindent to 'on' and smartindent to 'on' when you enter a buffer containing a perl file, and will turn them off when entering a buffer containing an html file.
Dropping the commands in a filetype file
You can also choose to organize things into separate ftplugin files in your runtime directory. If we want to continue with the perl and html examples above, you would do the following: In
setl autoindent setl smartindent
setl noautoindent setl nosmartindent