You have plenty of time for both but my wife and I have done (and will do again!) Bali -> Yogya -> Jakarta (CX 798 12am redeye to HKG) which means minimal flying/driving and maximum time at Amanjiwo. Last time we even had enough time to do the Borobudur dawn tour, some relaxing, and a wonderful picnic before heading to Yogya airport late afternoon for the Garuda flight to Jakarta. A long day but very memorable

In any case, you will find that the transfer between Amankila and Amanjiwo is pretty long and exhausting, lots of driving and pretty disruptive. At the wrong time of day you can encounter tons of traffic around DPS and/or Yogya (where roads are still somewhat in rebuilding from the Merapi eruption). That being said, Amanjiwo is absolutely worth the "trouble"!

As for different hotels on Bali, over 7 nights it is no big deal to switch hotels! The drive between Ubud and Amankila is not bad and there is plenty to see/shop along the way. I think these two areas are quite distinct and are each worth your time. Ubud town has become a little more commercial in recent years and Amankila is in a region with much less development.

Anyway, great itinerary, I'm sure you will have a splendid time no matter what. Feel free to PM.