I do not know if APT is able to use a PAC file directly but you can (with quite a bit of work/understanding) extract the relevant proxy information from the PAC file itself and use this information to configure APT to use a HTTP proxy.
return "PROXY proxy.some.site:8080; DIRECT";
Just look at your PAC file by entering its address in a browser. With this information you can create an APT configuration file:
sudo gedit /etc/apt/apt.conf.d/proxy
You should modify the file so that it contains the following information:
Save the file and the next apt-get run should use the configured proxy setting.
It would be nice if APT could work with PAC files because we also use them in our company. Perhaps somebody else knows if/how it works...
The Ubuntu Wiki Page for AptGet also has some hints how to configure a proxy for APT.
See also http://superuser.com/questions/323488/ubuntu-system-wide-proxy-auto-configuration-pac-script