hi-
I have 'only' used the Arduino 0018 IDE.
I took one of these CA-42 (pl2303) data cables, soldered the wires to correct pads.. (only 3)
and then used a 'header pin' that plugs into my breadboard.
I throw my Atmel chip in the breadboard, (tons of links/tuts on how to set this up), with crystal, resistors..etc..
main thing is a RESET switch.
I open the IDE....open my sketch..
upload sketch to my chip.. as soon as I see the 'text' at bottom of IDE saying sketch size..etc..
I hit RESET button.. works every time.