The 100MB partition on the spinner is probably from an earlier installation on the spinner. Just to make sure that there is not a dependency on that bootmgr, disconnect the spinner and boot from the SSD. If that works, then you can delete it.
There is always the danger that a bootmgr or BCD ends up on another disk - especially in your case where the spinner is on a lower port than the SSD.
If there is a dependency, the bootmgr is easy to move: Bootmgr - Move to C:\ with EasyBCD