How to develop a bootloader compatible application on S6?

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I want to use a custom bootloader in my application. I've done this before on AVR32Studio, this is just a new revision of an old application. So, my bootloader takes first 16k (used to take only 8k, but that's another problem...). On AVR32studio, it was enough to modify the linker script (in my case, the file from
FLASH (rxai!w) : ORIGIN = 0x80000000, LENGTH = 0x00040000
FLASH (rxai!w) : ORIGIN = 0x80004000, LENGTH = 0x00040000 -0x4000

Not enough on Studio6. If the bootloader is programmed and the boot area is protected, start debugging says "The flash region is locked". In my notes I can see that on AVR32Studio, I am supposed to use erase sectors instead of JTAG erase, but no such setting on Studio6.

So, either I need to find out how to make Studio6 to program only non-bootloader FLASH area (preferred) or how to link bootloader and application binaries together and program both when developing (if I must) or go back to AVR32Studio (please, tell me that I don't have to! Please!).

Thank you for any hints!