Q: I just upgraded to El Capitan.  Our photos are in both iPhoto and Aperture.  Is there a way to include both libraries in Photos (El Capitan)?

Use PowerPhotos or the iCloud Photo Library to merge them; if needed, launch Photos with the Option key held down and choose a different library.

(143670)

You can switch between libraries in Photos like you could in Aperture.  Hold down the options key while launching Photos. This will bring up a Library Chooser panel and you can select a differnet library.

Photos cannot merge libraries other than in iCloud (Notes on Merging Photos Libraries), but you could merge your libraries in Aperture before you migrate them to Photos. Aperture 3.3 or later can open iPhoto libraries as well as Aperture libraries and import an iPhoto Library into the Aperture library, see this document:   Aperture 3.3: How to use Aperture to merge iPhoto libraries

On El Capitan you do need Aperture 3.6.  Did you update to this version?  It is only possible, if you own an AppStore version of Aperture 3, see:   Updating to Aperture 3.6 After the Release of Photos

If you never updated beyond Aperture 3.1, you can only update to Aperture 3.6, if Apple Support will oblige with a redeem code, so you can download Aperture 3.6 from the AppStore.  There is nothing you can do on your own to update now, after Aperture has been pulled from the AppStore.