Hi,
Custom CSS is included from the options directly inline, after the main styling file. You can check if your changes are present right after being done by viewing the source of the site.
WordPress’ additional CSS field content is included the same manner, but a bit later in the source.
A delay in changes taking effect until a bigger change is done to the site is usually a clear indication of caching being present and not clearing properly (in some cases there may even be multiple levels of caching).