Hand winding smps transformer
1) Winding direction doesn't matter as long as you keep it consistent. If you are adapting a lathe or drill as a winder, the winding direction will be determined by the machine.

2) If the small windings are at approximately the same potential they can share a layer, otherwise you must provide sufficient insulation between them. Sometimes you may have to separate layers to reduce capacitance between them, or interleave them to reduce leakage inductance, but that is too complex to discuss here.

3) Winding coils side by side is simpler and provides better voltage isolation especially when the sections are different bins on the bobbin. That is essential for high voltage supplies and makes mains voltage safety approval easier. 

However it increases the leakage inductance, and that matters for high frequency applications like SMPS. The only reasonable way to know if you can do this is to wind one that way and measure the leakage inductance. If it's out of spec (or even close to it) wind another in layers and compare them.