The pickup configuration is part of the selected JTV model. Most modeled guitars have several JTV model variants, each of which uses a different pickup configuration. For instance, in the Lester (Les Paul) model bank the same model of Les Paul guitar is modeled in three different pickup configurations, corresponding to pickup selector switch positions 1, 3, and 5. Position 1 models the Les Paul with the bridge pickup alone; position 3 models the bridge+neck pickups, and position 5 models the neck pickup alone (or vice-versa; I get the position numbers mixed up sometimes). Pickup selector positions 2 and 4 in the Lester bank provide different Les Paul model/pickup configurations.

See the JTV manual for details of which guitars and their pickup configurations are modeled in each model bank/selector switch setting.

You can use Workbench (the Variax editor program) to change the models and load your custom models into your JTV.