I do not know how to set the fuses ...
There is more than one way to interpret this statement.
(1) I know what the settings should be but I don't know how to actually program the fuses.
(2) I know how to program the fuses but I don't know what the settings should be.
(3) I don't know what the settings should be but even if I did I don't know how to set them.
I think we are dealing with # 2 so I will proceed on that basis.
Google produced results on how to set fuses with AVR Studio but not with Arduino without bootloading it.
I think you are concerned with the fact that the published (http://www.codingwithcody.com/2011/04/arduino-default-fuse-settings/) Arduino fuse settings assume that there is a bootloader present and set the reset vector appropriately. When you program with the AVR ISP you wipe out the bootloader but the reset vector still assumes that the bootloader is there.
This is a valid concern and theoretically you should change the appropriate fuses which then makes the values from the aforementioned link invalid. What I have found is that currently this is not a problem. Apparently the hex codes in the unprogrammed bootloader area are treated as NOPs and the processor just proceeds through that area and falls into the program code area. In in other words I don't bother resetting the fuses when I switch from using the Arduino IDE with the bootloader to using the AVR ISP without one. I use the fuse values appropriate for the Arduino and just leave them set that way. Note that this operation could possibly change in the future.
Don