Order does not matter, you did not specify a distro or what boot loader you use. Years ago FreeBSD boot loader had no issues with linux, not sure if that is the case now. If using lilo you would specify Linux/FreeBSD as follows:
# Linux Partition
image = /boot/vmlinuz
initrd = /boot/initrd.gz
root = /dev/sda1
label = Linux
# FreeBSD bootable partition config begins
of cource it depends upon your partition setup.