If you prefer the old layout where custom fields are shown in single column vertically like before, use custom theme. You can either make your own custom theme or use pre-made one replicating the previous function.
Here is how.
Go to Extensions tab
Click Custom Themes
Find Vertical Fields Theme
Then click Install button.
When editing invoice, quote, order or other document, select this custom theme:
Now when you view the document, you will see your custom fields vertically:
Can you consider having custom fields that are empty not show on printed documents? I have a custom field on invoices named "Additional Details" and the label is visible on print screens even if nothing is entered into the custom field.
This change has been applied retrospectively, so opening, say, an old Customer Invoice, the original single column format for the custom fields is lost. A pdf of the original invoice has to be used.