Are you referring to the ARD agent settings? If so, start by looking at the help page for the kickstart utility. There's a lot that can be configured via scripts. Run this in Terminal-
sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -help
Apple also has a page here describing some of the options. Its old, but still applies since ARD hasn't been updated past version 3.x:
http://support.apple.com/kb/HT2370
kickstart -configure -clientopts -setreqperm -reqperm yes
Anytime I get stuck on a particular ARD configuration, I use the Create Client Installer... option in ARD to create a package with the specific configuration I want to use. Next, I take the package that ARD creates, open it up in Pacifist and then look at the postflight_kickstart_entries file. In the latest Pacifist, you would open the package, click the Resources tab, then go to (Package Name): RemoteDesktopClient.pkg: Scripts: Tools: postflight_kickstart_entries. That file contains the kickstart flags for that particular configuration.
Never used Pacifist, but it is awesome.
Thanks!