Grub will write to the boot sector of the disk you are installing Ubuntu right, not some other disk?
It can be installed to the boot sector of the current hard drive, or to the MBR. According to
this, "If you are installing Linux to a secondary hard drive, and no part of it will be on your main hard drive, then you must install GRUB to the MBR, and take your chances with Windows overwriting the MBR with its own at some future date. If this happens, you’ll have to use a Linux rescue CD to get GRUB reinstalled."
Grub is good about autodetecting every OS on the same hard drive. I can't say how it is with other drives since I haven't tried that.
Is there some freeware partition boot loader that is easy to use and will detect all 6 OS correctly without a hassle?
Grub would be your best bet there, I think.
Or would it be best to install each OS with the other hard drives disconnected and then manually mess with Grub, adding Windows and OS X to the boot menu?
Definitely install all the other OSes before Ubuntu (1) so that you do as little grub work as possible (2) so that windows doesn't have a chance to hide linux, as it enjoys doing.
I am really worried about my current windows boot menu being over-written.
You can keep using grub even if you don't have any linux installs. Works fine as a bootloader for windows.
Of course, you should keep a bootable dvd handy in case something goes wrong during your installs.