If you would like to build up your own Firewall (Hardware and OpenSource Software) i would suggest the following Requirements (rough edged)
Your Internet connection will be not even near your NICs physical capable throughput :) so lets just ignore the fact that a GbE connection is way enough.
If this Firewall would also switch/route internal connection, requirements will get a bit more interesting.
For your use case a simple Intel Atom or AMD APU would be enough. (just for routing and/or switching)
In case you want to something like DPI (deep packet inspection (via snort)) or Proxy servicing (via Squid) you'd need more power as every TCP packet, or whole stream needs to be analyzed and chosen what to be done with it.
As i mentioned in the beginning, a simple OpenSource software solution would be pfSense
pfSense provides you with an easy web GUI and package management.
And it qill run on every Hardware you'd have left around your office.
Just add Network cards to your own will (or the computers capacity) and start firewalling/switching/routing ect.
scaling with every service you run on the machine, you should consider adding more memory, more CPU or a Hard-disc for caching (proxy)
This Hardware is enough for my old school (where i do some IT work) and it has about 100 Simultanious users.
(just Routing, firewalling, and Proxy Server) ->
Ohh and on your question about PCI or PCIe
This doesn't matter at all, as the bus interfaces ar fast enough for a single GbE connection.
I you want to server 10 GbE then, i'd prefer PCIe :)
the same thing with onboard or extra card.
tho onboard card has the same connection to your northbridge/southbridge/cpu as an extra card. (depending on your architecture)