If you use an AWT Panel in your design, it uses FlowLayout by default, so you may want to switch it to XYLayout during prototyping.
When you initially add a new panel of any type to the UI Designer, you'll notice that the layout property in the Inspector says <default layout>. This means the UI Designer will automatically use the default layout for that container. However, you should immediately change the layout property to the layout manager you want to use so it is visible in the Component Tree and its constraints can be modified in the Inspector. You cannot edit layout properties for <default layout>. For more information on layout constraints, see Layouts provided by JBuilder
Usually you place a container in your design first, then add components to it. However, if you need to, you can draw a new container around existing components. However, these components won't automatically nest into the new panel. After drawing the container, you must explicitly move each component in the container. You may even need to move it out of the container, then back in. Watch the Component Tree to see when it nests properly. Each component inside a container is indented in the Tree under its container. If the component is at the same level of indentation with a panel, it is not inside it yet.
Even when you plan your UI first, you may discover three quarters of the way through that a particular layout you planned to use just doesn't work like you expected. This might mean backing up quite a ways in the design and using a different configuration of containers and components and layouts. For this reason, you might want to copy the container file (for example Frame1.java) to a different name and safe location at critical places along the way so if you do have to go back, you won't have to start completely over.
One thing that will really speed up your UI design work in the future is to create separate Java Bean components such as toolbars, status bars, check box groups, or dialogs that you can add to the Component Palette and reuse with no (or only minor) modifications.