You can reposition a portal by simply dragging and moving the portal using the header:
Tip: There is an option in the settings to allow portals to be dragged using the content area background. In case you have customized the settings to hide the header.
Alternatively, you can enter specific X and Y positions from the main settings window (click the taskbar icon to open it):
Tip: want to easily align portals? Turn on edge snapping in the App Settings:
This will turn on edge snapping, with a red line to indicate it will snap: