In general, what I remember from step up converters, is that they work more efficient the less they have to step-up. So a conversion from 4 to 12V is less efficient than a conversion from 8 to 12V.
But I also remember that after a certain input voltage the change in efficiency is only minimal. According to the datasheet of the MT3608 this seems to be around 4V.
Therefore I’d connect them in series, but I’m looking forward to other peoples input on this.