In Aptana Studio 3 (build: 3.0.8.201201201658) there is no Window -> preferences. If you have a .rvmrc in your project work directory, stating for instance:
rvm use ruby-1.9.3-p0@mygemset
... then Aptana should pick up the correct environment; in this case using ruby-1.9.3-p0 with gemset mygemset. Don't forget to run build install or build update (when you updated your Gemfile) from your project working directory path.
I must add that Aptana Studio 3 seems a bit buggy when it comes to picking up the correct environment, especially when trying to use ruby-debug-ide19.