You should Catalog Name Overwrites if some catalog (database) name is different in the 'real life' (production) while your dev catalog name is other. For instance you have Northwind in your Dev machine and NorthProd in your production server. In that case you should use
<mySqlCatalogNameOverwrites>
<add key="Northwind" value="NorthProd" />
</mySqlCatalogNameOverwrites>
You cannot change port, password or other connection string parameter in catalog overwrites. If you want that, just change you connection string in the .config file. If you don't know the port, user or password in advance (that info in known at runtime, like user input, etc) you could build your connection string at runtime and pass it to the DataAccessAdapter constructor, like:
using (var adapter = new DataAccessAdapter(myConnString))
{
//...
}
Hope that helps