Under Mavericks this should work fine. Once you have all the security details set in your VPN connection click on
Advanced and then
Make sure you select
Automatic Proxy Configuration and put the complete URL provided by your IT staff into the URL field. This will almost certainly be different to the proxy config file used by a computer that lives inside your network.
You don't want to send all traffic over the VPN. Now a web site internal to your network will use the proxy but those outside will not. This is the behaviour you want.
It may be useful to actually look at the .pac file. You can do that by entering the URL into the address field of your browser and it should be loaded as a text file.
The only case where you want all traffic to go over the VPN is if you are accessing an external web service that your organisation pays for that authenticates through the network - this is usually things offered by the library such as law services or special dictionaries.