Attached are screenshots of how to configure a Preset and a Toggling CC (Stomp).
In Amplitube you need to place your presets in the Preset Screen (SS attached).
In AT5, you need to set the FX Bypass per preset, globals are gone (SS attached).

In order to configure the stock FCB to control AT5 using the Ed Dixon Editor (or manually), you'll need to configure every pedal in every bank.
That's 100 actions. This is why most users opt for the UNO chip and ControlCenter Editor.