As mentioned in the Deployment Documentation, you do need to add some file masks for some file extensions so that all the needed files get deployed. This is partly because UnleasIt was released back in the 1.1 .NET days so it doesn't know about new 2.0 files like .Master, .skin, .browser, etc, but they can easily be added.
UnleashIt can deploy via ftp, but I always deploy to a local folder first then I use FileZilla to ftp files. After deploying to the local folder you need to edit the Web.config and set <compliation debug="false"...
You just set the source folder to the Web folder where you build mojoPortal (Release build for deployment) and set the destination folder to where you want the files to be deployed.
Its very easy.