The "three digit code" approach is used with many brands and models of remote that have many many sets of IR codes stored in memory. The "Six In One" or cable company remote is typical of that type. The particular button pushes and three digit code that you use retrieves these codes from memory and maps them onto buttons on the remote.
The Marantz remote is a totally different animal. It came from the factory filled with [only] Marantz codes, but it can be totally erased and programmed from the start. In fact, that's almost how I'd recommend that you do it.
Here's what I like: look around in the Files section for a system setup that you like, and modify it. Consult the FAQs about this.
Yes, you must download Marantz Touch Screen Setup (TSS) to program the remote.
DO NOT EVER try to stop a download in the middle, even if the software shows a button you can click on labeled "Cancel." That almost always throws the remote into a mode where you have to work hard to reflash the firmware, or to reload a .ccf. The process for both is found in the FAQs. There's more on this at [Link: remotecentral.com]