Hardik,
I strongly recommend that you watch the introductory webinars and look through some of the examples that come with your installation. There are a number of issues and unfortunately I do not have the resources to do one on one training.
Answers to your questions:
1. You do not need a profile for each layer the one profile is sufficient, it should be the cross section of your profile. I am not certain what you mean by stubs but your design has one waveguide and the design in the paper is a cross pattern. Use the linear waveguides and place them where you see the features in the paper.
2. In the design you attached you have a z-directed input plane and not an x. Additionally you have it set to Gaussian not modal for the transverse profile. Do keep in mind that the input plane must cross the waveguide in order to calculate a mode.
Something for you to be aware of:
1. Your resolution (set in the 3D simulations item within the project browser) is far too high. The auto setting is based on your source wavelength to ensure it is stable. However, you have feature sizes (in your case layer thicknesses) as low as 0.01. Your resolution must be such that the structure is properly discretized.
Scott