Just so you know, this is a very big topic.
First start by searching for hits on the term "embedded linux development" there are tons of references, and I don't have a real preference except to say don't buy swamp land in Florida as a reaction to any advertisement search hits. The better point there is "don't buy anything" all information is free, and while there also is information available for purchase, I feel you should review the voluminous free information first before you decide to purchase content, so you can evaluate the worth of any purchased content.
What you'll find is that the total summary of running Linux is defined as using:
- Bootloader
- Linux Kernel
- Root File System (RFS)
Then it becomes the varieties of:
- How to select a bootloader
- Whether to build/customize a bootloader or use a standard one
- How to customize the Linux kernel
- How to build the Linux kernel
- How to customize drivers either by selection, configuration, or modification/re-compilation
- How to establish or obtain a root file system and manage it
- That this all matters on a "per processor" basis a moderate amount, especially when you consider the $9 computer which is ARM based versus x86 architecture
At some point during all this, you should install a Linux desktop distribution to a full up system computer, such as a moderately modern laptop or a desktop system. A very helpful package to install is build-essentials, and it may be already on there depending on the distribution. Then you can learn how to compile, how to use the tools for building and understand how this process works. You can also read up on how to just recompile the kernel for the particular distribution you have installed and play around with that to ensure you understand enough about the topic.
Next I'd purchase one of the cheap, hobbyist boards such as the Raspberry Pi or the BeagleBone Black and use the kernel and distribution they provide. Install the tools so that you can recompile that kernel. Install the tools so that you can recompile that bootloader. Learn about how to build your own RFS and place it on that hobby target.
Along the way you'll have numerous, more specific questions and I encourage you that once you start getting these more specific questions to absolutely create more threads.