In SharePoint it is possible to configure the Primary and Secondary site collection administrators from SharePoint Central Administration. It is also possible to configure them from the Site Collection Administrators page under Site Settings.
What is the difference between these two? Does it matter in functionality if a user is added to one vs the other?
As both routeNpingme and Aaron indicated, there isn't a practical upshot from a privileges perspective. Whether an account is added to the Site Collection Administrators group from the site collection provisioning area (in Central Admin) or from within the site collection admin options (in the site collection itself), the resultant permission and privilege set is the same.
There is a big difference worth noting, though, and that revolves around e-mail notifications. In previous SharePoint versions, the "Primary Site Collection Administrator" (as identified by SharePoint within Central Admin) was actually referred to as the "Primary Site Collection Owner." The current version of SharePoint no longer refers to the primary and secondary admins (from within central admin) as "owners," but I believe the underlying behavioral aspects remain the same.
Primary and secondary site collection owners are also site collection administrators, but they receive e-mail notifications pertaining to quotas, user access requests, automatic site deletions (if such behavior is enabled), etc.
For more information, this link: http://technet.microsoft.com/en-us/library/cc288243.aspx. The reference is for WSSv2, I know, but the behaviors are (again, I believe) the same. This is corroborated by the following links for WSSv3 and MOSS 2007 on Microsoft's Office site: http://office.microsoft.com/en-us/help/HA101577811033.aspx. Note how the "Manage unused Web sites" section at the end of the page specifically states that the site collection creator is the site collection owner, and that e-mail are sent to the owner and secondary contact.
I hope this helps!
There is some internal difference (does not affect anything). The effective permissions is the same when you set a site administrator in "Site Settings" versus "Site Collection Administrators" in Central Admin. For example you can set just a primary site collection administrator and add in additional under site settings and they won't show up in Central Administration.
No difference, they both become site collection owners. :)