You can follow this tutorial to create the the appxbundle.
Then in the windows iot device portal, select add button to install your app like this:
After that, you will see this Dialog:
Select browse option to find your app bundle and make sure "I want to specify optional packages" selected like this:
Add all the dependencies(.appx). If you're building for MinnowBoard Max, they are in dependencies\x86
path. If you're building for Raspberry Pi 2, Raspberry Pi 3 or the DragonBoard, they are in dependencies\ARM
folder.
After that, select next will start the install process. After the process is done successfully you can see your app in the apps list of device portal.