How to import older Aperture photo library after setting up new Photos app and a new library
There is no way to import an Aperture/iPhoto library except start a new Photos library and have it convert from an existing Aperture/iPhoto library.

I think the best solution would be to start a new Photos library based on your existing Aperture library. Attach your iPhone to the Mac and wait for it to appear in the sidebar in Photos, then import everything it will let you from the phone. Finally, set it as the system library (Photos menu > Preferences > General tab > "Use as System Photo Library") and enable iCloud Photo Library (Photos menu > Preferences > iCloud > iCloud Photo Library).

In theory this should cause the images from your new combined Photos library (old Aperture library + what was on the phone) to upload to iCloud, while also downloading anything in iCloud that does not exist in your new Photos library. And in turn, your phone should download anything new that is uploaded to iCloud.

The step of syncing from your phone directly to the Mac should not be necessary, but is a backup just in case iCloud freaks out with the change in the System Photo Library and removes what you uploaded from your phone. It also saves Photos from having to download any of those photos, assuming it finds them to be duplicates of what's in iCloud.