We will soon be adding the RSP Jupyter notebook interface to the QuickStart, which should give you a more natural feel here.
However, the recommended way to do this would probably be to use the Terminal in RStudio Server Pro. Then you can just run pip install --user <pkg_name> from the RStudio Server Pro terminal. Are you familiar with the RSP terminal? Does that help solve your problem?
It at least saves the trouble of SSHing into the VM.