Yes, you can install FreeBSD manually. It will work if you will done the process correctly.
Also you can copy your running system to another HDD.
Assuming MBR and UFS you should do something like this:
fdisk -vBI /dev/newhdd1
bsdlabel -wB /dev/newhdd1s1
Edit (save, edit, restore) a created bsdlabel if you need it.
Run newfs for every data partition (enable softupdates and journalling if you need it)
Extract the kernel, base to new boot partition (or copy existing system to new disk).
Mount new / partition somewhere, edit fstab, rc.conf and some other if you need it.
You can run newly installed system as a jail inside the main system. Using a jail you can install some software or prepare the new system for future use.