The second pass of binutils will be installed once you enter the chroot jail. At the point that it is installed, you will have libraries installed in /usr/lib and /lib inside the chroot and these will be the libraries you will eventually build all the software against.
I am just at chapter 5 now, and the time to enter the chroot environment is on chapter 6. So i think the libraries should be install in /tools/bin .The /usr/bin and /bin directory is belong to the host system.
The ld that is built is not installed until you are inside the chroot. Once in the chroot /usr/bin and /bin refer to the newly built LFS system and not your host.
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