If you are not sure about layout, you do not feel confident to do it, but you have to do it, then just follow recommended design rules from design guide. You do not have to understand everything, if you follow the rules it will work.
Still, if you are not sure, you can start slowly:
Project 1: Copy & Paste layout from reference board
Project 2: Do the layout by yourself, but do it almost exactly the same as on reference board (use same layers, same pins, ...)
Project 3: Do some pin swapping, choose layers, do not break rules
Project 4: Do everything by yourself, break recommended rules, simulate
On more projects you work, more information you will learn and more confident you will feel.
To answer your questions:
1) See above
2) This is hard to explain. More you work on projects, more you will get an idea of what is important. Sometimes I try to imagine how currents will flow or how fields around tracks will be created (I had electromagnetic fields subject at university), but I am not sure if you have to study it for standard board design - that may be needed if you have to break too many rules (e.g. you design very small / large boards). Otherwise you should be fine with following rules and without deep theory of understanding - use common sense. Also, for many things e.g. crosstalk, you can simply just use an online calculator, deep theory may not be required. However, it is always very useful to know how some peripherals work - e.g. how the read / write of memory interface is done.
3) Normally I do not simulate. If you follow design rules, from my experience the board will work oki. I only simulate if I have to break too many rules and even for this I am very limited as I do not have any simulation software. If I have to simulate, some of my clients have Hyperlynx - that is what I use. Usually I run DDR wizard, have a look at eye diagram or try crosstalk simulations.
4) I learn from
design guides - Intel has the best ones, but these are very hard to get as you only get them when you work on Intel designs and they are all under NDA. However, you can find some which are free e.g. try to google for "imx6 design guide" or "com express". Here is an example:
http://cache.nxp.com/files/32bit/doc...6DQ6SDLHDG.pdf