> Do you know of a good tutorial online that can explain keystores/truststores 
> and certificates well?

For theory, there is no substitute for
http://java.sun.com/j2se/1.5.0/docs/guide/security/jsse/JSSERefGuide.html,
in particular the parts about the KeyStore and TrustStore interfaces.
It was only after lots of problems that I finally broke down and read
it, and I've been far less frustrated since.

For practical how-to reading,
http://www.jasig.org/cas/server-deployment/solving-ssl-issues might be
of help.  If keytool is scary or limiting, you can try
http://portecle.sourceforge.net/ for a GUI keystore management tool.
Additionally, there's a good CLI tool, keystore, that we developed as
part of http://code.google.com/p/vt-middleware/wiki/vtcrypt that has a
number of helpful features beyond keytool.

Hope that helps,
M

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