Question really asks it all. I want to apply a GP to the Domain Administrator account, but when I go to GPMC, you don't see the default OUs like Computers or Users listed.
Can I move the account to a new OU without breaking a system dependancy?
Yes; this is safe (and, in fact, recommended) unless you have anything pointing to the account that uses the LDAP path (usually a third party application - Microsoft is pretty good about using the sid instead).
The reason these aren't visible in GPMC, by the way, is that they aren't technically OUs.