If you use the contentPath or dirPath providers, the directory that you specify in the source argument will be created on the destination computer if it does not already exist. If you choose the contentPath provider, you can use its includeAcls=true
setting to copy the acls over.
Here's example syntax:
msdeploy -verb:sync -source:contentPath=c:\inetpub\wwwroot,includeAcls=true -dest:contentPath=c:\inetpub\wwwroot,computerName=Server1
For the permissions to be set correctly, you must use domain accounts or have local accounts with matching SIDs on both the source and destination computers. For more details, see the contentPath article.
If you want to set permissions on the destination folder separately, you can use the setAcl provider. setAcl has settings like setAclUser and setAclAccess that allow for more granular control. See the article for more details, including the ins and outs of permissions.