Some controllers like the AT*X*MEGA series support individual flash sections that can be programmed/erased independently. However, with the ATMEGA2560 this is not possible.
One way would be to concatenate the .hex files as part of the build process. This can be achieved with some modifications to the makefile.
Something similar to this
all: $(TARGET).hex
srec_cat bootloader.hex -intel $(TARGET).hex -intel -o combined.hex -intel
Flashing the ´combined.hex´ would then include both, main application and boot loader. There is a related discussion on AVRFreaks.
Regarding the fuses, you just have to make sure that the boot loader (address) stays configured as the entry point.
EDIT: You can use this fuse bit calculator to verify fuse settings. Select your device and make sure "Boot Reset vector Enabled (default address=$0000); [BOOTRST=0]" is enabled with your current high fuse value. You currently use
mega2560.bootloader.high_fuses=0xD8
so that seems fine.