There are two different scenarios:
1. You have a web site "Default Web Site" on the destination under which you are trying to create a new app "MyWebApp". This can be done.
msdeploy -verb:sync -source:iisapp=C:\mywebfolder -dest:iisapp="Default Web Site/MyWebApp"
2. You Do not have a web site on the target and you are trying to create a new web site and then create an app under it as "New Web Site/MyWebApp"
For this you would have to first create the site from some default site on your local system or the remote box and then create the app under it
msdeploy -verb:sync -source:apphostconfig="Default Web Site" -dest:apphostconfig="New Web Site",computername=remotePC,username=uid,password=pwd
msdeploy -verb:sync -source:iisapp=C:\mywebfolder -dest:iisapp="New Web Site\MyWebApp",computername=remotePC,username=uid,password=pwd
Let us know if you need more info.