Difference between "Primary DNS Suffix" and "Connection specific DNS Suffix"?

 Primary DNS Suffix is set for the entire computer and will be used on any network adaptor on which no Connection-specific DNS Suffix has been defined.

The Connection-specific DNS Suffix allows us to overide the Primary for a specific network adaptor so that when your computer registers itself with the DNS server it's presently using, it will register with a well-formed fully qualified domain name (FQDN).  The thing that MS calls DNS suffix is really just everything to the right of the first dot in a FQDN.

Imagine your company-supplied laptop computer has FQDN "joe.boston.corpX.com" and it's part of an Active Directory domain at the office.  It's Primary suffix is "boston.corpX.com" and it's name is "joe."  When you boot it up at the office, it will DHCPDISCOVER an IP address and the AD DC's DHCP server will respond, then your computer will register itself with the DNS server on that AD DC using it's FQDN.

If you use a VPN Client on the road, though, so you can connect to your company's network from the hotel broadband service.  It may be smarter (or neccessary) to have your computer register itself as joe.remote.corpX.com with the RAS server in your network.  That's where the Connection-specific DNS Suffix comes in.  When you installed that VPN Client Software (or your IT team did), it created another network adaptor and the Connection-specific DNS suffix on that one is ... yep, remote.corpX.com and all is well.

In general use, we don't use it.  On systems with only one network adapator, just leave it blank.  Unless someone in a higher paygrade that knows why you should change it tells you to, that is... :-)