You can long press bubbles to edit them. This brings up the bubble edit screen:
If you just want to move bubbles away from the favorites cloud (i.e. watch face) just select a different cloud on the top: archive or a folder.
When you move the first bubble in a folder the folder will be created where the bubble used to be. But you can then long press on the folder and move the folder to the archive.
You can also hide bubbles. In fact, app bubbles can only be hidden. You’d have to uninstall the app to remove completely. But to hide use the button with the red-X to do that. More on this here:
Hidden bubbles are visible for a while, so you can unhide them if you made a mistake:
Use the option “show hidden bubbles” to control the visibility of hidden bubbles:
How to restore hidden bubbles: Missing app icon on the watch
To delete watch face complication bubbles, you can scroll to the bottom of the Bubble Edit screen and select “Delete”. More on this here: