The MTJ plugin in the Builder allows you building a specific junction type (metal-insulator-metal) indeed.
Building a general structure can be done using other Builder tools. In principle, you can build any structure in the Builder. For example, you may build a multilayer oxide structure using the Interface plugin by adding oxide layers in a step-by-step manner, see
http://docs.quantumwise.com/tutorials/ag_au_interface/ag_au_interface.html for how to use the Interface plugin, and then match the oxide heterostructure to the Fe electrodes, using the same Interface plugin.
Note that you need to consider optimizing the separation distance between the neighboring oxide layers, as well as between the oxide stack and metal electrode. This can be done in a set of separate calculations for individual interfaces, and then building the entire structure of the MTJ device. Afterwards, you may still do additional geometry optimization of the entire central part of the device, if needed.
