Two DC DC converter with different output - In series or parallel?
Both methods are certainly used. Serially connected DC/DC supplies are usually used with "high" input voltage such as mains. You first get 12V (or something) from the rectified 230VAC input and then you convert that to 1.2V or something. 

Certainly the flyback can have multiple outputs but unless they're multiples of each other wound in a particular way you're going to hurt on cross-regulation. 

So in this case just put them on parallel. Depending what you have on 5V you could actually use a linear regulator on that, just be aware that you have 1.4x power dissipation on regulator. 

Also 3A output is nothing to sneeze at, it's entering territory where ripple currents and losses start to matter. You could use the TI webench or just copy one of the many similar examples on-line. 

Bottom line, connecting DC/DC supplies in series kills your efficiency as instead of 85% you now have 85% of 85% (72%) and so on.