How do I apply proxy settings automatically on all the workstations?

Very simply.The easiest way to do this is to configure a workstation to have the correct settings for the proxy server and other details such as any sites which should bypass the proxy. Then use this machine to edit the policy settings under User ConfigurationWindows SettingsInternet Explorer Maintenance. You can directly import the "Connection Settings" from the machine you are on if you need to, then check and edit them before clicking OK to set them in the policy.

Alternatively you can just configure the "Proxy Settings" to set the proxy server address and exceptions list (to exclude sites such as your intranet from having to go through the proxy unnecessarily). You would also want to look at the various security settings under User configuration Administrative Templates Windows Components Internet Explorer to lock down the IE interface to prevent users from changing the settings themselves.