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You need to connect members in such a way that their centroid should coincide. If your frame members are not connecting with each other at centroids, than use the option "insertion points".

True, there can be certain cases where UBC gives a higher base shear. However, without knowing basis of study, parameters involved and data points/ no of runs and sensitivity of each parameter quoted results, it hard to conclude. Keeping numbers apart, there are other differences too. IBC considers seismic design category which affects your calculated base shear whereas UBC considers your seismic zone only. While designing a hospital in a lower seismic category, you may end with a higher base shear than for a commercial building with a higher design category, both comparisons being done for IBC. As I said, it is not an apples to apples comparison, and your results can be different based on what parameters you consider. To me, the whole exercise is pointless, because basis are different. Number crunching.

I have attached tutorials that will show you how to setup ETABS model for dynamic analysis. Go through all tutorials. There are lucid and self explanatory. OneDrive-2014-03-09.zip

You can find solved examples in the books such as Dynamics of Structures by Anil k Chopra, and Seismic and wind design of concrete buildings by S.K. Gosh and David Fanella.