There are many ways to navigate your maps and switch the context of your views based on the task you are interested in. Furthermore, moving your workflows between 2D and 3D can benefit from best practices to avoid instances of unexpected behavior. The following set of lists are categorized recommendations of best practices and tips.
General
I cannot select my features
If you have imported a map, globe, or scene document with some layers set to be not selectable, those settings will be honored on import into ArcGIS Pro. Click List By Selection 
on the Contents pane and see if any items are unchecked. You can also go back to the original document and change whether you can select from layers, save the document, or import it again. Layers that are not selectable will remain not selectable when imported to ArcGIS Pro.
Get started with 3D
ArcGIS Pro has the benefit of providing maps and scenes to work side by side. At the same time, a greater awareness of how your 2D data behaves in a 3D environment can help you work through any issues you might be seeing.
I have moved my 2D point features into the 3D layer group, but they are drawing embedded in the earth.
For 2D layers to appear 3D, utilize 3D symbology, and display properties, the first step is to move the layer into the 3D Layers group of the Contents pane. The reason your points may now appear sunken into the earth is because the anchor point for that point in 2D made sense as the centroid of the circle. However, in 3D, the centroid doesn't. To place your points on the ground, you should move the anchor point. Open the Symbology pane for that layer to format the point symbol and click Properties. Scroll down to find the Position setting and expand the Anchor point presets. Choose Center bottom for the point to reposition on the ground instead of partially beneath the surface.
The map (.mxd) that I imported seems distorted or has position issues when converted to a global scene view.
If the spatial reference of your map is not WGS84, then a local scene view is recommended to avoid the distortion from being reprojected for global scene views. If you plan to view your maps in a 3D space, you should consider changing your default scene view to open in local mode, rather than global mode. You can change this by clicking the Project tab and clicking Options. Click Map and Scene and make Local the default scene view setting.
I have polygons that I added to my scene view. They look strange when I move them into the 3D Layers group.
When a layer is shown in the 3D Layers group, it renders its geometry separately from the rest of the scene. This means that polygons can flicker or stitch with other content in the scene. This display conflict is especially common with the ground surface mesh, which is always changing to reflect the best level of detail for the current view location.
You can improve the display of the polygons by extruding the layer to create volumes or changing the elevation properties to separate (vertically) the polygons from other content.
In some cases, you might be best served by moving the layer back to the 2D Layer category.
Navigation in 3D
I've zoomed underground and want to return to the surface.
If you ever end up somewhere you don't want to
be, click Previous Extent to return to your previous
location, or click Full Extent 
to see all of your
content.
If you've just been turned around, you can press N to orient yourself to the north, or press P to look perpendicular to the horizon in scene views. This would be like looking straight down from the top of your view.
For specifically zooming underground, below-ground navigation is disabled by default for the layers in your scene; this helps you avoid accidentally going underground. If your scene contains data that correctly belongs underground, you should enable this capability (for example, pipelines or geologic bodies). In the Contents pane, select the Ground elevation surface. On the Appearance tab, in the Surface group, check the option Navigate Underground.
I want to click the sky in 3D to navigate.
The interactive Explore tool relies on a 3D location—either on the surface or on a feature—to provide a control point for handling navigation events such as pan, zoom, and rotate. When you click the sky, the tool cannot determine how far away you want to go.
To zoom up or down in 3D, you can either use the U and J keyboard shortcuts or set an explicit height offset in the height box in the bottom corner of the view.
When panning it seems like my view is sliding.
Automatic panning gestures may be enabled in your project if you see your view slide in the direction you are panning. This can be useful if panning greater distances to move farther faster. In 3D, this can look like you are rotating or spinning the view. If you don't like the glide, click Project and click Options. Click the Navigation tab and uncheck Enable Panning Gestures. Panning will become more static and the view will stop panning as soon as you release the pointer.
I want to quickly zoom to my selection.
Whether you have interactively selected your features by dragging a shape or clicking in the view, or performed a selection query, there are many access points to quickly zoom to your selection. From the map itself, you can quickly zoom using the bar at the bottom of the view. Click the Selected Features count in the corner of the bar to zoom to the selected features. This includes all selected features from all layers. To zoom per layer, right-click a layer on the Contents pane.
In a table view, you can right-click a row and click Zoom to Selection or switch back to the map or scene view associated with the table and click the Selected Features result count as described above.
Zoom To Selection 
is also available on the Map tab, in the Navigate group.