It's been a while since I posted this question and I thought that I would stick up what I've found since for anyone who needs this question answered.
I now use Leiningen to manage my projects though I have started playing around with cljr which is a repl and package manager that complements it. Either of these make it much simpler to generate a runnable jar file.
Taking Leiningen as an example set it up using the instructions on the site and then call lein new in your workspace. This will create a folder to house your projects as well as a sub-folders for your source and tests a readme file and a project.clj file.
Edit the project.clj with the dependencies that you will be using. Dev-dependencies are dependencies which you need purely for development such as swank-clojure shown in the example below.
(defproject myproject "0.0.1-SNAPSHOT"
:description "My Personal Project."
:url "http://example.com/my-project"
:dependencies [[org.clojure/clojure "1.1.0]
[org.clojure/clojure-contrib "1.1.0"]
[**other dependencies**]]
:dev-dependencies [[swank-clojure "1.2.1"]]
:main [org.myproject.core])
I find swank-clojure useful as you can then type lein swank to start a swank instance which you can connect to via emacs.
:main defines what namespace contains the -main function.
Calling lein uberjar will create a standalone jar which will then run.
Hopefully that helps anyone who had my problem!