SouthernAtHeart:
Then once I have the Arduino boot loader on the TQFP Atmega328, I could finish populating my board and load sketches over serial via an FTDI cable?
Sure. Typically you'll do it afterwards via an on-board ICSP header as others have already mentioned. But, on the first all SMD board I designed I only added an FTDI header, so I built an adapter ala TQFP 32 Pin Socket Mount by ril3y - Thingiverse.
My only regret is not building a complete target board (with ICSP header, resonator, 10k resistor and de-coupling caps) but this worked fine for me. If you've got more money than time, check out the stuff on eBay (search for TQFP32 and find, among others, http://www.ebay.com/itm/QFP32-TQFP32-FQ-FP32-PQFP32-TO-DIP32-Socket-Adapter-/230726458579?pt=LH_DefaultDomain_0&hash=item35b85e5cd3).
And soldering these things isn't that hard, especially if you can do 0805 (or even 1206) passives. Just remember that the solder wick is your friend. I try and solder each pin with a minimal amount, but always go back thru with the wick to remove any excess (as well as any solder bridges).
It's not that hard really.
FWIW,
Brad
KF7FER