To use VEP as an FX rack, you use the Audio Input plugin. I don't know what DAW host you're using. But you instantiate the instance of VEP first in order to connect to it via that plugin. It's more involved in Logic than it is in Cubase iirc.
Once in VEP, you instantiate the type of Input channel "Input" and connect to it in the dialog from Audio Input (the other type, "Channel" is for sending an output from an instrument channel to an Aux bus type, ie., to process it separately). Now you have [both kinds of] automation you may set up, Host Automation or MIDI, found in separate tabs in the Automation Mapping dialog, which is accessible via F5 or from the View menu.
So the two types are for [mostly] mutually exclusive use cases, the FX rack paradigm, as _not_ an instrument type is not dealing with note-on or note-off data but will take control data from a MIDI track or event. The other is just an extension of an instrument in VEP. Both, however are automatable exactly the same way.