First of all...
1) How are you "Inspecting" md0? Have you mounted it somewhere? Does it even have a filesystem on it? Can you write to it as root?
2) Ignore that for now. Automount might do strange stuff.
3) If I remember right, md0 should not stop existing unless you disassemble the array or reboot.
4) There is no need to edit your fstab file and risk ruining your system if you have a seperate boot partition on your ssd. At least not, before you can manually mount your raid device and EVERYTHING is working fine. Also, don't change the existing lines unless you really want to change your existing mounts. I thought you only wanted to *add* a mount? I still don't understand why you mess with your SSD if it's not part of the array.
5) Why are you rebooting / what are you expecting? Also: Sounds like you did something wrong in mdadm.conf. Also you might be (accidentally) trying to boot from raid and have forgotten to add the needed modules or hooks or simply just to regenerate initrd?
. I still would like for the SSD to be independent from the rest of the storage, so perhaps just partitioning it right would work?
I don't understand... I thought the OS was already running on your SSD (which is not part of the array)... and that is supposed to stay that way? Why repartition it / change it / even touch it?
You should provide a lot more information so someone can help you. Like your fstab file, your mdadm.conf, output of the commands while you manually assemble the array and mount it... etc... if you're not getting enough information to figure out what your problem is you're probably not using the tty enough.