Help is pretty infrequent around here but in time you get some help I'm sure.
1/4) From what I know you will need to let the Arduino do the boot loading ( as you mentioned in 4 ). You should not need an isp but its a nice to have for sure. If you write to the chip with an isp your by passing the Arduino firmware. To write your code you would have to use an Arduino boot loader app. I'm guessing it comes with that or is available. There is a GUI flash tool called FlashTool.exe if Arduino does not have its own.
3) You should not need any of that, as burning to the chip would over right all the Arduino stuff.
2) You do know the "hex file" is your compile code right?
with out that Arduino stuff
[ bootloader : v-usb : your code ] using a USB boot loader
[ v-usb : your code ] burning to the chip from avr studio or avrdude.
With Arduino
[ bootloader : Arduino : v-usb : your code ] using a USB Arduino boot loader
1/4) From what I know you will need to let the Arduino do the boot loading ( as you mentioned in 4 ). You should not need an isp but its a nice to have for sure. If you write to the chip with an isp your by passing the Arduino firmware. To write your code you would have to use an Arduino boot loader app. I'm guessing it comes with that or is available. There is a GUI flash tool called FlashTool.exe if Arduino does not have its own.
3) You should not need any of that, as burning to the chip would over right all the Arduino stuff.
2) You do know the "hex file" is your compile code right?
with out that Arduino stuff
[ bootloader : v-usb : your code ] using a USB boot loader
[ v-usb : your code ] burning to the chip from avr studio or avrdude.
With Arduino
[ bootloader : Arduino : v-usb : your code ] using a USB Arduino boot loader