Setting a mark using Vrapper is the same as in Vim. Press the m key followed by a lowercase or uppercase letter.
There is a slight difference. If you use a lowercase letter, the mark is set as an invisible mark, like in Vim. However, if you use an uppercase letter, the mark is also set as an Eclipse bookmark. It even appears in the bar on the left as a visual bookmark. Bookmarks set this way can also be viewed by using the Bookmarks view.
Tried with: Vrapper 0.52.1, Eclipse 4.4.1 (Luna) and Ubuntu 14.04
Many editors and IDEs allow the user to bookmark one or more lines and jump to them later. In Vim, this is implemented as its mark feature. For those of us who would like to visually see which lines have a mark, Vim offers nothing.
The vim-signature plugin is a perfect solution to this problem. Just install it using Pathogen and the marks you will place will be displayed in a new column to the left of your code. There are many other features of this plugin, but I think the visual marks is key.