ISP Custom ATmega168 board with Atmel AVR ISP MKii

I'm building a board that basically combines a pro-Mini with an LCD and a few other things. What I'm trying to understand is what the best way to program the uC will be. I was thinking about programming it directly (no bootloader) with the MKII. However I've never done this before and am not clear on the details. I've seen tutorials on how to Bootload a chip with the MKII, but are there any good tutorials on how to program directly with it? And can I still program in Arduino IDE/use arduino libraries? I'm a bit hazy on what exactly happens during compiling and the referencing of libraries and all that.

Thanks,
Rich

It is quite easy to use an MKII to program an Arduino. I do this quite often. Arduino 1.0 supports it out of the box. If you want to understand what is going on inside you may want to switch on the "verbose" settings and have a close look at the output.

Does that mean that I can program in IDE and use all the libraries? So if I'm doing that the 6 Pins I need are Vcc, Gnd Reset, MOSI, CLK, and MISO, correct? And then there would be no point in having the software reset function on there so I can get rid of that, correct?

Thanks!

Yes, that's exactly how it works.