Designing flyback converter - multiple isolated outputs
Can I treat 2 secondary coils with dual voltage output as one with
  double voltage for the purpose of calculations?


With a flyback converter, energy is stored in the primary and released to the secondary at a rate dictated by the switching frequency. As most Flyback converters are DCM types, the output voltage produced depends entirely on the load resistor, the duty cycle, the input voltage, the frequency and the primary inductance: -



Picture source.

Regulation of the output voltage is performed by using feedback and this counters the effects of a varying load by applying greater or less duty cycle thus, it controls output voltage by increasing or decreasing the energy transferred per cycle.

However, for flyback converters with multiple outputs you have to be more careful. If one load suddenly takes less power, the other output voltage will rise and, in order to keep that voltage regulated, the energy throughput is reduced and the first load (that took less power) may become significantly reduced in voltage due to regulation feedback occuring on the 2nd load.

It's certainly worth modelling your load variations in something like micro-cap or LTSpice to see what happens.


  However for LT converters that use flyback in primary as feedback the
  formulas for feedback resistor(s) are based on Vout and turns ratio.
  How do I apply these?


Assuming that method works fine for a single output (and it does but isn't quite as good as direct feedback) then you still have the same basic problem of what happens when loading imbalances can occur.