After opening a file (File->Open) with places these are displayed on the map. When you click them there is an option to see some more information. There should also be an option to save the place in the bookmarks.
On a click with the left mouse button, a popup shows more information. This one could have a bookmark icon next to the print icon in the top bar to do that. Alternatively there is the right mouse button click which shows a context menu and already has an "Add bookmark" entry. This could be improved however to use the information of the item beneath the mouse position - it's exact position (instead of the mouse position) and it's name for the name of the bookmark. Last but not least we could change the implementation of bookmarks in Marble such that placemarks could be bookmarked directly and would inherit their properties, as opposed to seeing a bookmark as a new placemark that might share its position with an existing placemark. This would mean some rather big internal changes though. I'm leaning towards the first option, adding a bookmark icon to the info dialog (PopupItem class), because it seems the most consistent option to me and also straighforward to implement. Opinions, anyone?
Yup, go for the first option. It gets the job done perfectly. Although, a tool to import all placemarks on a file into the bookmarks would also be useful.