It is possible to combine Tor with tunnels like VPNs, proxies and SSH. The traffic can be sent through both Tor and the second tunnel, in either order. However, this is an advanced topic and appropriate only for special cases. Adding a second connection does not automatically improve security, but it will add significant complexity. The potential positive or negative effects on anonymity are being controversially debated [archive].
The Whonix project remains technologically neutral in the anonymity discussion. The improper combination of Tor and another service may actually degrade a user's security and anonymity. One such case is using a proxy to hide Tor network traffic from your ISP.
While proxies are a type of tunnel-link they should not be thought of as a replacement for a VPN and SSH in this configuration. This is because connections to proxies are unencrypted and therefore should not be used to hide Tor use. Proxies are ok for circumvention of censorship if that has been shown to work from the users location but are unsuitable for hiding Tor due to lack of encryption.
Combinations of tunnels-links with Tor are difficult to set up and should only be attempted by advanced users. For the vast majority of Whonix users, using Tor in isolation – without a tunnel-link (VPN, proxy or SSH) – is the correct choice.