cd to the boost source directory, then create symbolic links to the toolchain. Add ./ to the head of your path, to force the stupid "jam" system to use the cross tool chain.
cd boost_1_34_1
ln -s `which avr32-linux-g++` g++
ln -s `which avr32-linux-ar` ar
ln -s `which avr32-linux-ranlib` ranlib
ln -s `which avr32-linux-as` as
ln -s `which avr32-linux-ld` ld
export PATH=./:$PATH
./configure --prefix=/usr/avr32-linux
make
make install