Let me explain.
Left Side = updated model, newer model
Right Side = old model, model that you want to update.
During model merge, it is the model that you want to update, model where you want to apply the changes from Left Side model. (Default direction is Left -> Right)
During alter script generation, it is the model for which you want to generate the changes. You may have noticed that on page Right Model (for alter script generation only) there is the option Reverse Engineering Alias. It allows you to connect to the database directly. (In previous version, you had to reverse your database first to create a new physical model and then compare the two physical models. Now it is not necessary.) When to use it: Let’s say you updated model in TDM and now need to connect to database, compare the differences and generate alter script to synchronize the model and database. The updated model is Left Side model (you open the Sync & Convert Wizard from it) and on the Right Side page you can connect to the db directly now.
So, let me say again:
Left Side = updated, newer, modified model
Right Side = old model, model that you want to update/generate alter script for.
If you have any questions, please write me back. Thanks.