This highlights my reasoning behind first applying the eclipsed DoT then the non-eclipsed one, as you are more likely to have both DoTs carry through to the next eclipse as the eclipsed DoT gets refreshed but the non-eclipsed DoT does not. Note: the lunar shower buff only affects the direct damage not the ticking DoT damage.
I double checked this over at elitist jerks and found this (under advanced techniques of Hamlets' Moonkin guide)
"When casting two DoTs at the beginning of Eclipse: first cast the Eclipsed DoT, then the uneclipsed DoT, then Starsurge if it's up. In Lunar, cast Starfall before all other spells since its DPS drops when Eclipse ends, unless you're using the DoT clipping technique, in which case you cast it after the Moonfire."
Source:
http://elitistjerks.com/f73/t130885-...ced_Techniques