Most of the time when you are forced to access a system through an intermediate hop it is fairly trivial either manually or automating it with ssh config. That is assuming you are using *nix. When using putty this is also possible and here is a quick note on what I did.
First off ensure you have a working ssh key to the intermediate host you will be using.
Next setup and save your new putty session as you would for any other connection.
Under Connection -> Proxy pick Local and set the Proxy hostname to your intermediate host (I set port to 0 but port does not matter).
Under local proxy command set something like this:
plink.exe %proxyhost -l root -agent -nc %host:%port