Dear anurag,
without seeing at least a sketch of what you plan to model and knowing the targets of the analysis (see also ATENA Troubleshooting, 2.1.1), it is hard to recommend to work in ATENA Engineering or ATENA Science+GiD.
In general, if you only need (quasi-)static analysis and all curved surfaces (if any) can be reasonably approximated with flat segments, it is usually easier to create the model in ATENA Engineering (3D or 2D).
For basic information about connecting neighbouring volumes, I recommend to read Troubleshooting, 2.2.14 I have problems when using the Interface (GAP) material on contacts.
We also generally recommend to proceed with the corresponding ATENA Tutorial example (Science/GiD, Engineering 3D, Engineering 2D) before starting with your first own model.