How to selectively rsync folders while retaining tree structure?

Good question. You need to use the -R or --relative flag. From the man page:

-R, --relative Use relative paths. This means that the full path names specified on the command line are sent to the server rather than just the last parts of the filenames. This is particularly useful when you want to send several different directories at the same time. For example, if you used this command: rsync -av /foo/bar/baz.c remote:/tmp/ ... this would create a file named baz.c in /tmp/ on the remote machine. If instead you used rsync -avR /foo/bar/baz.c remote:/tmp/ then a file named /tmp/foo/bar/baz.c would be created on the remote machine, preserving its full path. These extra path elements are called “implied directories” (i.e. the “foo” and the “foo/bar” directories in the above example).