What I do is move the unzipped dragonruby folder (since it has some invisible stuff) to my development folder and rename it. From there, the text files and the documentation from the mygame project get moved into a documentation folder, and samples are moved into an examples folder. That pretty much takes care of the non-runtime stuff - other project folders and resources are (re)added to the development folder as needed.
The dragonruby executable will use the mygame folder if you don't provide a name, but you can use any name you want as a parameter. Previous commands are available in the Terminal history, so it is easy to reuse them.
As for gems, standard RubyGem support can be problematic in any custom Ruby implementation (such as the Game ToolKit and RubyMotion), since they may not have all the classes and/or methods, and often don't include all the shared libraries. Test and debug gems even more so, since they are mostly expecting the regular MRI Ruby.