An example command to move your asp web site "Default web site" to a server "Server" as "new Web Site" would be like:
msdeploy -verb:migrate -source:metakey="default Web Site" -dest:metakey="New Web Site",computername=server,username=YourUserName,Password=PassWord
1. By default when you deploy your asp files to the server using Web Deployment Tool the files will be replaced/added/deleted based on your situation. If you want the files to be backed up then you can do that manually before starting the migration process. Its preferable that you back up your metabase (IIS 6) or config (IIS7) too.
2. If you want to run these pre and post deployment steps as part of the migration process you can wait till RTW of msdeploy is released (soon) where you should be able to run pre and post deployment scripts and commands based on your needs as part of the deployment step
3. Web Deployment Tool also enables you to add rules to skip certain files, certain types of files or skip newer files etc.
To know more about these and other commands you can read here
Let us know if you need more information