Well it depends what settings you want to change. If you are referring to simple configuration changes in IE they are usually in the registry. You need to research and figure out where in the registry they are and then you can create a batch file to make the change using REG.EXE. You can also use the LANDesk Package Builder to make a registry change. Ir ecommend looking at the Users Guide that comes with the software for more details on specifics.
As far as learning the product, I can recommend a few items for you.
First, the Help file in the console is very useful.
Second, you can find the manuals for LDMS here:
Third, searching for the words "Best Known Method" or "BKM" in the community can bring you to many useful documents for how to use the features within LANDesk.
Information about LANDesk's training offerings can be found here: http://www.landesk.com/Support/Training/Index.aspx