Add manually installed android apps to Google Play account
Sideloaded apps are not linked to Google Play. You will have to update them manually (i.e. sideloading)

What you could do is install Titanium Backup (needs root), and use its Attach to Market feature.



Another solution would be to use AppBrain instead of Google Play, because AppBrain scans the apps in your phone, and informs you of any updates.