One favored approach to deploying to a server is to use Git or GitHub. This basically involves logging into your server, moving to the directory you want to run your app from, then cloning your files directly from GitHub. You then build your app on the server. This approach ensures that platform specific files get built correctly, but requires that Meteor is installed on the server (500+ MB), and can result in slightly different builds wind up in production if your servers are slightly different.
cd /var/www sudo git clone http://github.com/myaccount/myapp.git cd /var/www/myapp meteor build --directory ../myapp-production sudo service myapp restart