If I ordered the base MacPro($2799) and and downgraded to One 2.8GHZ Quad-Core Intel Xeon making the price $2299 would the motherboard in my system still have 2 cpu sockets?
Apple charges $500USD for the second processor. To do it yourself, you have to obtain the correct CPU cooler as well as a second CPU. You can't do this for $500. Apple Care would also not cover a 2nd CPU not installed at the factory.
The 2.8GHz CPUs cost ~$850 retail. The heatsink costs ~$100. Apple give you $500 back when you downgrade. So at current pricing it would cost you $450 extra to upgrade. That pricing probably won't change much. Maybe in a few years it would come down some, but then this isn't a high volume part. I imagine most of them are in Mac Pros so the ones that do appear in places like eBay will probably be sought after and fetch high prices .
You also void your warranty by installing a second processor. So if you want 8 cores buy the 8 core now. You can save money by going with a refurb or used system.