The best way to learn how to use a new processor and/or toolset is to get on and build something in hardware or software or both.
Here are a number of projects, starting with some simple hardware and software. As they progress, so more features and resources are used and new features of the development tools and processor hardware are used.
Possibly the hardest are also the simplest. These are the first two where a working processor board needs to be built and the first software project must be built. Once the basics have been learnt, everything else should build on those so it is important not to skip the earlier tasks.
If you have a development kit and/or some ready-built hardware, you can use that. Clearly, there are going to be some differences that are way beyond my ability to predict and, unfortunately, you are going to have to figure those out for yourself.
The starter hardware is based on the H8/3664 processor. This is pretty well the only one available in something other than a surface mount package (although not in a 0.1″ pitch) which gives you the chance to construct a board of your own without any etching or other complication.
As an alternative you could use the BasicMicro BasicATOM Pro 24-M board which is built around the same H8/3664 processor. This board is built onto a 24 pin DIP carrier that can be plugged straight into a breadboard for prototyping. Not all the pins of the 3664 are brought to the outside world but more than enough are available to get a good idea of the capabilities of the chip. It comes with a Basic interpreter built in but can be programmed in C using the same tools described here. The flash downloader will be different as the BasicAtom uses a different method to put the processor into boot mode. Find out more at www.basicmicro.com