You'll need to separate out your application layer from your database layer, and that means specifying the MONGO_URL. Which means running your app through the bundle command, uncompressing it, setting environment variables, and then launching the project as a node app. Here's how...
#make sure you're running the node v0.10.21 or later
npm cache clean -f
npm install -g n
sudo n 0.10.21
# bundle the app
mkdir myapp
cd myapp
git clone http://github.com/myaccount/myapp
meteor bundle --directory ../deployPath
cd ../deployPath
# make sure fibers is installed, as per the README
export MONGO_URL='mongodb://127.0.0.1:27017/mydatabase'
export PORT='3000'
export ROOT_URL='http://myapp.com'
# run the site
node main.js