You can, and you should, post logs even if you can't post links, just remove the part, without them it's hard to know what you're doing wrong.
General tips
- Don't bother using Astral communion, you don't need the extra burst in Emerald Nightmare, BotA saves you a button to push and does the job.
- Think ahead! Nature balance let's you keep the dots rolling on your target without having to cast them too many times, plan on having an empowered wrath if sunfire is going down and plan having an empowered Lunar strike when moonfire is going down.
- If you are moving soon (example you just recieved Rot on Nythendra) pool 80 ap so you can cast 2 starsurges while you position Rot away and come back to the boss.
- If you are not moving from your position anytime soon, dump your AP. Cast your moon spells on CD so that you can spam Starsurges.
- Targets that die in less than 8 seconds are not worth dotting, just cast wrath or new moon on them and let someone else (melee for example) finish the job.
- Flask of the whispered pact + Suramar surf and turf OR Azshari salad + Potions of the deadly grace OR Draenic intellect potion (cheaper)
To answer your questions:
1. Wasted AP is worse than wasted empowerments. Also, if you have to make this choice, you're poorly managing your AP generating spells.
Starsurge is our main source of damage on most fights, so wasting AP means you're throwing away dps.
2. New Moon, Half Moon and Full Moon give you 10, 20 and 40 AP respectively, so if you are at 30 or more AP when you notice you have 3 MoonMoon stacks, you'll have to cast Starsurge at some point. Keep in mind you should never have 3 stacks of MoonMoon except during pull.
3. Personally I use Shadowed Unit Frames, which I customized a little to track dots. Maybe there are easier things.