My boyfriend and I want to get married.  If we do this at the
courthouse, just us and the judge, and not tell anyone.  If we do
this, will we then be allowed to have a "proper" church wedding, with
all the correct vows etc (we're episcopalian), so that to the
assembled family and friends, it looks like this is the "first" time
we're getting married, and it is in the eyes of God, as our families
would expect?  With the whole separation of church and state, I'm abit
confused.

Hello.

Even if you've already been married at the courthouse, you can still
have a church wedding.  Since you mention "the whole separation of
church and state," I'm assuming that you're in the United States.

Basically, if you were already married in a civil ceremony, you're
perfectly free to have whatever sort of church ceremony that you want
provided that you can get a church to go along with it.  Different
churches have different requirements.  Some churches won't do a
full-blown, formal wedding for a couple that has already been married
in a civil ceremony, especially if a long time has elapsed since your
civil wedding.

So how does the "whole separation of church and state" thing apply? 
Well, you don't need a church or clergy person to have a legal
wedding. The state does not require anyone to have a church wedding. 
On the other hand, the state can't stop a church from setting its own
rules. Thus, a church is free to refuse to do a wedding for certain
people (e.g., those who are already married).

You mention that you're Episcopalian.  The Episcopal Church DOES do
weddings for couples previously married in civil ceremonies. The
Episcopal Church has a special procedure called "Blessing of a Civil
Marriage."

sources:

"The Blessing of a Civil Marriage"
http://www.dandello.net/bocp/bocp4.htm#page433

"Civil marriages may also be blessed in the Church. This provides
couples with an opportunity to include a witness of their brothers and
sisters in Christ to their commitment."
source: Trinity Episcopal Church
http://www.trinityexcelsior.org/worship_weddings.html

"What to expect in the Episcopal Church"
http://www.vts.edu/2001/marriage/episcopal.htm

Newsgroup message archived by Google Groups:
"Subject: Re: Can we still have a church 'wedding'? "
http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&selm=386F82BC.8D9E5879%40mail.utexas.edu

Of course, there's no requirement that you have your "proper" wedding
in the Episcopal Church. If the sort of ceremony that they're willing
to perform for you isn't what you want, you're free to shop around for
another church.  Legally, the marriage that counts is the one for
which you get the license.  See:
"What Makes Your Marriage Legal"
http://www.foreverwed1.com/sitemap/marriagerequirements.html

search strategy:
episcopal, wedding, "civil marriage"

I hope this helps.  If anything is unclear or requires amplification,
please use the "request clarification" feature. Thank you, and best
wishes for your marriage!