You should not be putting your custom CSS into the files directly – any plugin update will clear them either way. Either use your theme custom CSS field, or some themes have a custom.css file, or your can also use the plugin custom CSS input (Theme Options -> Custom CSS).
You can still override !important rules with higher specificity CSS rules, for example.
div#ajaxsearchpro1_1 .probox .proinput form input.orig {
margin: 12px !important;
}However I rather recommend adding margins either to the parent form or to the .proinput element if you can. The !important rules are there for compatibility reasons.