I am trying to set up Pekwm on a new computer. The old one was very old (when GKSU was still available).I've got tint2 and conky and everything else working fine but I need help with polkit and how to launch things that need root privileges.
If this is possible I'd be grateful for any help.

The way polkit works AFAIR is that packages deposite text files in /lib/polkit2 or some such tree. One of these files will list all the actions that the package recognises, and another will set default polkit permissions for these actions: which ones are allowed to all users, which are allowed to active users only (those who control their own console), which need authentication with user password or administrative password, and so on. You can create override files in /etc/polkit2. There's also a file in this directory which specifies what counts as an administrative password (root obviously but it might be wider). I think most of these use the same syntax as desktop files.

There's a polkit daemon that is launched at boot and a polkit agent which collects passwords; if the desktop doesn't provide one, polkit uses its own (rather ugly) text-based one which comes up in an xterm