The easiest way is to add a ICSP header to your project and then attach a programmer to that header after the IC has been soldered in place. There are TQFP ZIF sockets you can get to program the chip before soldering, but they can be pretty expensive. If you add the header to your design you can add a bootloader plus make future firmware changes to the chip if needed.

We usually run the chip at either 8MHz or 16MHz, which are the only officially supported speeds in the Arduino IDE. You can either use an external crystal or the internal 8MHz clock. While you can run it slower (4MHz, or 1MHz), I've not seen it run slower than that, so I'm not sure the 32kHz clock will be much help. You will need an AVR programmer of some kind to update the fusebits to switch between internal and external crystals (and use the internal clock divider if needed). After that you should be able to upload the Optiboot bootloader (make sure it is compiled for the correct speed). Also check out this tutorial on installing a bootloader. As for different programs, the Arduino IDE is pretty easy to use although does have its limitations. If you are using a non-standard configuration it is fairly easy to create a boards.txt file with the relevant information so the IDE can use it. AVRdude is also a pretty good program and is actually what the Arduino IDE is built on. Keep in mind it is command line so might be tricky. And don't forget the official ATMEL Studio.

We actually buy these and use them on quite a few boards (about 10k per month), but had enough requests that we sell the individual ICs as well which is probably why we are not an official distributor. Our primary supplier is Future Electronics although we've also been known to buy them from Digikey, Mouser, Arrow, and directly from Atmel. If you have any other questions please feel free to email techsupport@sparkfun.com and they help you out.

These are actual Atmel ICs and are fully functional according to the Atmel datasheets.