Hi,
custom.css file should be used to add custom css modification, so the code from this file overrides other css rules.
In your case if you add this code into custom.css:
.ajax-indicator {
left: 50%;
position: fixed;
top: 100px;
margin-left: -64px;
}
These values will be used instead of the values from template.css - it's useful, because during future template update, your modifications from files like template.css (and other edited template files) will be lost.
Cheers
Joshua