Absolutely, you have two main ways to do it, and one way you shouldn't.
Fix: For different foods with different times/temps, use SYNC FINISH. Set the time and temp for Basket 1, then set the (different) time and temp for Basket 2. Press SYNC FINISH, then START. The basket with the shorter cook time will wait (showing HOLD) so they finish together.
If that didn't work: You can also cook them completely independently. Just press START for one basket. While it's cooking, press the other basket's button, set its time and temp, and press START for that side. They'll run on their own schedules, but the SYNC functions won't be available.
Heads up: Don't use SYNC BASKETS for different foods—that function copies the same time and temp to both sides. Also, strong smells can transfer, so maybe don't do fish and cookies at the same time.