How are Digital Certificates Stored and How Do I Manage Them?

I'm trying to learn about Digital Certificates. I've been doing
research on the web for several hours, but I still have a million
questions. Here are a couple:

1) Where are digital certificates stored? Is every certificate stored
in a file on my drive somewhere? Are the private keys and public keys
stored separately?

2) Is there a utility I can use to manage certificates? I've learned
that I can view certificates using the Microsoft Management Console
application Certificates.msc. However, that utility seems to be
deficient in one important respect -- it doesn't distinguish between
my certificates (certificates for which I have a private key) and
others. Is there a better utility?

-TC