I asked this same question here and on the Photos board a couple of times and never got a clear answer.
I prepared by merging the Aperture libraries from both my iMac and Macbook Air in Aperture using Aperture into one library on an HDD. Then ran some Duplicate finding software on it and tried to cull the results before continuing. But the software added a bunch of keywords. The software added a bunch of keywords to certain pictures which were meant to help create Smart Albums, but it wasn't a very intuitive solution or workflow.
So I finally just gave up and pulled the trigger on using Photos. I renamed the resulting merged file Photo.library on the HDD and copied it over to both the iMac and the Macbook Air. I did the iMac upload first (Download Originals to this Mac-checked). It took more than a week to "process the library and complete the up/download of about 20,000 photos and video to the iMac. The resulting System file which the Photos app requires to be set was Photo.photolibrary on my iMac.
After all had been uploaded it seemed to be working OK, my Aperture Projects had migrated to Photos as iPhoto Events in the sidebar ....and are now considered Albums in Photos.
(@apple please choose a nomenclature and stick with it!)
But once I had waited around seemingly forever and everything had up loaded, it seemed to be working smoothly (i.e. photos i took on my iPhone would appear quickly in my Moments and I learned quickly to drag the photos to the "Albums" in the "iPhoto Events" sidebar to sort them.)
Then I turned on the Macbook Air Photos app, this time with the "Optimise Mac Storage" checked. BTW anticipating this move, I had already upgraded my iCloud storage to 200 GB which I'm sure Apple is targeting with this "innovation".
Once the MBA Photo app was turned on, t took another week or more of processing and uploading to get that photo library up to the iCloud.
But I had learned patience from reading the many ******* here at this very site.
finally, it showed me that everything had been updated. the problem was that the file/photo count on each machine didn't match my Photos on iMac reports19,636 items while the MBA version reports 19,565 items.
The previous advice of others here about using the File>Import command is good. the app seems to be able to detect if the photo is already in the library.. I haven't found many duplicates in the stuff I migrated directly, but I haven't looked closely, and I'm tired of mucking around with this crap. However, I did find a bunch of photos had been deleted... File>Show Recently Deleted and I know I hadn't deleted them myself. On both machines under this option. Checking out some of them, There was quite a large number, they seemed to be duplicates which leads me to believe that the apple servers are doing some kind of dupe checking. it'd be nice to hear from Apple on this.
Anyway FWIW, logging on to the iCloud website just now and waiting for it to update, it shows I have 19,564 photos and videos. Close to my MBA but still 100+ off from my IMac. My iPhone and iPad I run from the MBA so those match up.