Get yourself a real ISP programmer. Best is the Atmel AVR ISP MKii ($34 at mouser.com) but others will work as well.
I used this one from MDFLY for a long time before I got a MKii to deal with '1284 chips.http://www.mdfly.com/index.php?main_page=product_info&cPath=5&products_id=415
Need to make simple 10-pin to 6-pin adapter to use it (connects +5, Gnd, Reset, SCK, MOSI, MISO from the 10 pins 2x5 layout to the ISCP 2x3 layout)
and a simple 2-line addition to programmers.txt file
Others of similar type exist from several sources: sparkfun, adafruit, nkcelectronics. I've accumulated several types in the last couple of years, never got around to checking them out. Just used the mdfly programmer & USB/Serial adapter (an FTDI Basic) and now just use the MKii becasue I didn't want to dig up 2 sets of cables; had the MKii and its cable out, so I just used that.
My boards all have 16 MHz crystal, two 22pf caps, 10K reset pullup resistor (with diode across it when I remember, anode to +5, cathode to reset, like current Uno), and 0.1uF (100nF) caps on Vcc & Avcc.
Select board type of Uno, and let 'er rip.
I burn the Uno bootloader first to make sure the fuses are set correctly.
Then you can download sketches via USB/Serial adapter after that, or use the programmer and File:Upload Using Programmer, blows away the bootloader and your sketch starts immediately.