Hi Alieev,
Certainly! Simply check the Primary key checkbox at all fields that should be in the Primary key in the Software Factory, Datamodel > Tables > Columns. More info here: Data model | Thinkwise Documentation (thinkwisesoftware.com)
The Software Factory will upgrade the table for you when you start and finish a whole Creation cycle (Generate definition, Validate definition, Generate source code (Smart or Full, both work), and lastly Execute source code).
If data needs to be migrated, you can use Data migration to determine how old fields should be mapped to new fields. More info here: Data migration | Thinkwise Documentation (thinkwisesoftware.com)
In more complex scenarios, you can even opt to use an Upgrade control procedure. More info on that here: Functionality | Thinkwise Documentation (thinkwisesoftware.com)