sorry, i don't quite catch what you mean, but i'll try:
there are two possible places for a boot loader to be installed; in the master boot record, and in the boot sector of a particular partition (primary partition, that is). windows will always install the nt bootloader in the front of the partition that windows is installed in. after all, that loader is needed to boot windows itself. then, that partition will be marked 'active.' if there is no boot mechanism (boot loader) found in the mbr, it will automatically attempt to boot from the active partition. however, i do know that there are times when windows has written to the mbr, taken over it, and made the computer go directly to that windows partition, instead of booting any other os. (is that all the time? i think so)
i know that if you install windows on a secondary hard disk (i.e. not the primary boot hard drive), it will install windows and ntloader onto that second hard drive, but it _still_ writes to the mbr on that primary boot hard drive; so when the drive is booted, it will 'forward' the computer to the right ntloader on the right drive. (happened on my old laptop that had a heat damaged primary hard drive)
when you install grub (i haven't used lilo in a long time, but i assume the same applies), you have a choice to install it in the mbr, or in a particular partition. so, if i had, say, the freebsd boot loader in my mbr and still wanted to use that as my main loader, i could install grub right into its linux partition and have the freebsd loader chainload it. (or actually, the freebsd loader may even be able to natively boot linux. dunno; never used the freebsd loader in the mbr)
grub has to boot a windows partition by chainloading (booting into the boot loader on a particular partition)... one reason being that it can't read ntfs. but the main reason is that grub itself can't boot a win32 kernel. it doesn't know how to; so it has to call on ntloader to do it.
and on the other side, ntloader cannot directly boot linux. (naturally. it's microsoft...) so with that bin file, you're creating an image of the boot sector of your linux partition - where grub is installed - and having ntloader boot that, which will trick it into loading up grub. and grub knows how to boot linux.
so if you're doing any cross-win32-os booting (grub->windows, ntloader->linux, etc), you will have to chainload from one boot loader into another. that's due to the incompatibilities of the two different OSes, not because of the location of the installs.
even if you have ntfs and xp in your first partition, and linux in the second, the ntloader is in the boot sector of the first partition. so you could leave ntloader in control (meaning the mbr automatically forwards booting to ntloader in the boot sector of the first partition), and use it to boot windows directly, and have it use a bin to connect to your linux partition. or, you could put grub in the mbr, have that boot linux natively, and have it chainload from the mbr to the ntloader that resides in the boot sector of your first ntfs partition.
erm... i hope i didn't confuse anybody. (most importantly, i hope i didn't confuse myself and mix something up...)