When you create a new server in Deploy, the first deployment will always be deployed from scratch. This is great when you're starting afresh however not if your server already contains the latest revision.
For example, the latest commit in your repository is ddec653d and the files up to reference ddec653d are already on your server, and you want to create a new server in Deploy but you don’t want it to re-deploy all the files that already exist on your server. To do this you would set both the start and end commits of your initial deployment to commit reference ddec653d. Once this is done Deploy will assume that your server contains all the files up to revision ddec653d and will only deploy files from this revision on the next deployment.