This procedure is slightly different for 2.2.x and 3.x (with the 3-stage boot) systems.
The general idea is that you copy the first sector of your native root FreeBSD partition into a file in the DOS/NT partition. Assuming you name that file something like c:\bootsect.bsd (inspired by c:\bootsect.dos), you can then edit the c:\boot.ini file to come up with something like this:
[boot loader] timeout=30 default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS [operating systems] multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Windows NT" C:\BOOTSECT.BSD="FreeBSD" C:\="DOS"
For 2.2.x systems this procedure assumes that DOS, NT, FreeBSD, or whatever have been installed into their respective fdisk partitions on the same disk. This example was tested on a system where DOS & NT were on the first fdisk partition, and FreeBSD on the second. FreeBSD was also set up to boot from its native partition, not the disk's MBR.
Mount a DOS-formatted floppy (if you have converted to NTFS) or the FAT partition, under, say, /mnt.
# dd if=/dev/rda0a of=/mnt/bootsect.bsd bs=512 count=1
Reboot into DOS or NT. NTFS users copy the bootsect.bsd and/or the bootsect.lnx file from the floppy to C:\. Modify the attributes (permissions) on boot.ini with:
C:\> attrib -s -r c:\boot.ini
Edit to add the appropriate entries from the example boot.ini above, and restore the attributes:
C:\> attrib +s +r c:\boot.ini
If FreeBSD is booting from the MBR, restore it with the DOS fdisk command after you reconfigure them to boot from their native partitions.
For FreeBSD 3.x systems the procedure is somewhat simpler.
If FreeBSD is installed on the same disk as the NT boot partition simply copy /boot/boot1 to C:\BOOTSECT.BSD However, if FreeBSD is installed on a different disk /boot/boot1 will not work, /boot/boot0 is needed.
Warning: DO NOT SIMPLY COPY /boot/boot0 INSTEAD OF /boot/boot1, YOU WILL OVERWRITE YOUR PARTITION TABLE AND RENDER YOUR COMPUTER UN-BOOTABLE!
When the FreeBSD boot manager runs it records the last OS booted by setting the active flag on the partition table entry for that OS and then writes the whole 512-bytes of itself back to the MBR so if you just copy /boot/boot0 to C:\BOOTSECT.BSD then it writes an empty partition table, with the active flag set on one entry, to the MBR.