Photo cleanup after ios8 migration

I have an iPhone 5 running ios8, and a macbook laptop running OSX 10.9.5
Even before the migration away from camera roll, my iPhoto library on my mac was problematic. I was also running the iPhoto app on my iphone. A lot of times when I backed up to my mac, I would end up with duplicate photos, so I bought Duplicate Annihilator and have used it a couple of times.
So I think I am not backing up the photos correctly, which to me, is the most important stuff on my phone.
Now that I've migrated to "Photos" my photo library is a hot mess. The photos are all out of order, jumbled together, I can't find anything, and there are photos missing or unfindable in Photo that I have written off as gone forever, but when I open another app to attach a photo, the correct photo sometimes turns up there. Also I have photo albums that are empty that I cannot delete.
Ideally, what I would like to do is move every single photo and album out of my phone completely, organize them all using iPhoto (or maybe even Lightroom at this point since iPhoto's organization is a bit counter-intuitive anyway and if the iPhone doesn't play nice with it, then I may not even want to use it anymore), and then upload certain photos back into "Photos" on my phone.
And then moving forward, when I take a photo on my phone, I would like it backed up to my mac once only. Or iCloud, I'm not super-fussed about which way, the nightly iCloud backup is easier, but at some point I need to import the photos onto my Mac, correct?
but I clearly have gone off the rails somewhere about how best to back up to avoid duplications. I don't want to lose anything, I prefer to manage the photo deletions from my mac vs. my phone.
I don't need any fancy family sharing or anything like that, just a simple way to get this stuff organized and stay that way! And I can't seem to find any info on that for post-iOS8.
Sorry for the long complicated post. I spent most of last might trying to fix it and I couldn't get anything to work. Maybe I should back up and wipe my phone completely at this point? (shudder)

If you don't need the items you've identified in either of those two folders, it is safe to remove them. Items in your home folder are generally safe to remove unless they are in use by an open application or process.
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