You can configure AdvancedPortals to use WorldEdit instead of the Selection Tool from AdvancedPortals.
To enable the integration (add and) set the config option
WorldEditIntegration to "true".
This will disable the commands
/portal wand (or
/portal selector) and will use cuboid selections from WorldEdit instead.
Select Portal as WorldEdit selection
You can use
/portal we-selection with a portal name to select the portal as cuboid worldedit selection.
This command becomes available when WorldEdit is installed.