For the first backup (to create the initial IDR file) you should go ahead and archive everything on the machine. It's the recommended approach and you are even prompted to do so after the first IDR file is generated.
After the file is created and you have performed the first full archive, you can then go back to selecting whatever you want for your normal job rotation.
Just remember, the reason you are using IDR is to rebuild the server from the tape media in the event of a DISASTER...thus, the name. If you decide not to back up some of the important files/folders (ie. the WINNT/Windows directory, various archaic-looking DLLs, etc...) IDR may become useless.
Hope this helps.
