You should to do 2 loads, 1 for the initial FULL Load, just like you do it now and another one for the daily incremental loads.
Check your primary keys and find a way to make a SELECT query which will return your new/modified rows. You need another query which will show you which rows had been deleted / modified as you need to remove these rows before adding the new/modified rows into your db.
To run this automatically you need to right click on your job and select "export Job" It will build your job into a JAVA JAR file. With a .sh and .bat launcher. You can then use the windows scheduler to execute this daily, or use CRON to execute it daily if you happen to have a linux server.