How to change preferences in Chrome by modifying files?

There is a file called "Preferences" within the "User Data/<Profile>" folder that appears to contain these settings. The location of this file varies according to OS. For the "Default" profile this is located at:

WinXP:

C:\Documents and Settings\<User Name>\Local Settings\Application Data\Google\Chrome\User Data\Default\Preferences

WinVista:

C:\Users\<User Name>\AppData\Local\Google\Chrome\User Data\Default\Preferences

You then need to search for the appropriate setting in that file. I would close Chrome (and backup) first as this file appears to be updated automatically as you navigate tabs.

"Enable Auto-fill to fill in web forms in a single click." appears to be stored here:

   "autofill": {
      "enabled": true,

"Offer to save passwords I enter on the web."

      "password_manager_enabled": true,

The policies are most likely pushed by GPO. These are located in the registry under HKCU\Software\Policies\Google. You can try to modify them all you want, they'll just get put back in at the next GPO refresh.

Saving passwords is not something your administrator "forgot" to turn on - it's on by default. Your administrator deliberately disabled it - because it's an incredibly lame feature that is insecure and allows users to forget their passwords. It really has no place in an organization.