PuTTY does not store its configuration in a file. However, PuTTY can use a "proxy command", as described here.
In your case, the example config file shows that there should be two encapsulated SSH connections:
The outer SSH is done to host
login.nets.***. When that connection is done, the command
nc is run on that host: it basically forwards data bytes to port 22 on the inner host
The inner SSH is done again from your machine, to host
zeus.nets.***, with all data bytes sent through the outer SSH.
ProxyCommand option, the
ssh login part is the invocation of the outer SSH when the user (or your GUI application) tries to connect to "zeus". It is not obvious whether
PuTTY itself can be invoked that way: there is a command line but you also need the "inner PuTTY" to forward all its bytes to the "outer PuTTY", and it is unclear whether that "outer PuTTY" will accept the bytes on its "standard input" (Windows is not Unix, and, moreover, PuTTY does not expect to run in a terminal or on raw bytes; it more tries to open its own window).
Try to use port forwarding. In that case, you manually start a PuTTY to
login.nets.***, with a port forwarding from local port 5000 (that's an example) to remote host
zeus.nets.*** and remote port 22. Then you configure your GUI to talk (with PuTTY) to
localhost on port 5000. When the GUI launches the PuTTY which connects to
localhost on port 5000, the other PuTTY (the one you started manually) forwards the bytes to host
login.nets.*** with instructions to open a connection from that host to
zeus.nets.*** on port 22.
This may or may not work, depending on the configuration of the SSH server on
login.nets.*** (support for such tunnels can be enabled or disabled by the sysadmin).
Use a more Unix-like SSH client, e.g. through Cygwin. Since this is the usual OpenSSH, it will be able to read and use the provided SSH configuration file, and do the nested invocation. Of course, there is no guarantee that your "SourceTree" application can be configured to use such a SSH client.