Design and build a single board computer
AFAIK, there is no good overall source on designing a Singe Board Computer (SBC). You might find some some specific help in manufacturers applications notes.

Develop your skills by doing small, specific, low-cost projects. IMHO start off small, and you will learn faster, with less cost or frustration. 

(Telescope makers saying: "What's the fastest way to make a 12" telescope? Make a 4" telescope first.")

Start with MCU's which are simplest to get working. Then add external memory via an MCU with an external memory interfaces. Then ethernet and USB to get accustomed to them.

You might start with something where you might get lots of help, like an Arduino.

Plan to make several projects. Aim to get each one working properly. Expect that some might be hard, or not work. The biggest surprises are the things we do not imagine. Making something work properly, rather than partially work, helps find the biggest surprises.

Try to decide on a time-scale for a project, and stick to it. It is very easy to be over optimistic, then when everything takes longer, ignore that learning. IMHO it is better to set some target, recognise the things that took longer than expected, and learn from it.

Expect to take 6 months or more, so don't try to do too much in a single project. Even if you can do this full time, there will be tasks which rely on others, and take longer than expected. Because they are out of your control, there isn't much that can be done (other than throw money at them).

Unless you have easy access to test equipment, expect to spend more on tools and equipment than on parts and PCBs. Be prepared to buy development boards; having a way to test and verify behaviour saves a huge amount of time. Even for a DIY board, having a working comparison helps a lot, and pays back in unexpected ways. 


Research what you can of existing designs. R-Pi is probably the easiest to find out about. Reuse good ideas. Manufacturers publish some application notes for specific part families which may help.
Increase your competence with a PCB design package. BGA packages are likely to need more than two layer board, so Eagle is less useful than other free alternatives. If possible find a few PCB design packages. Try them for a few days, and decide which you like, by trying to do a project. There are some guides on the net from manufacturers about how to design boards for MCUs or low noise. Make it more challenging; try to make boards with large and very small track/space in a restricted area. Practice on simpler boards should pay off later because you'll more quickly see how to place parts to make routing easier.
Surface mount soldering. BGA packages are hard. Start with similar pitch, but easier packages like LQFP, then move to UFQFP, then BGA. Design and make something, preferably using 2-layer PCBs, so that you can experience how to make, debug and get them to work. There are useful MCU's available in all those packages for a few $. 
Cultivate a PCB manufacturer. Look for service with a good reputation, and with the specs you think you'll need. A low-cost, small volume, PCB service like OSHPark might be worth cultivating. I found laen at OSHpark very helpful. 
Designing debuggable hardware. Practice. Review each project when it is complete and working. Each project will teach something. Keep a 'log book', or written record to remind yourself of what was hard, easy and surprising in each project, as well as how you did it. 
Practice bringing up an OS on a SoC. How would you bring up e.g. Linux on a new board? You can practice that using an R-Pi or BeagleBone. Once you have this under your control, you could move onto SoCs which you want to use, or have much less support. (Or stay with SoC's with lots of OS support already.)


Edit:
If you have a very clear idea about which SoC family you want to use, and the same manufacturer makes MCUs in much lower-frequency parts (TI, STM, Freescale, etc.) then you might want to start with their MCUs. That way you'll become accustomed to reading their documentation, using their forums, and also you'll start to get a feeling for how hard their products are to use.