Yes, you can add multiple waypoints as needed.
It's worth noting that if you just drop two points, one for your start position and one for your finish location savvy navvy will provide the best route based on wind, chart and tidal data.
If however you want to ensure you go "via" a specific point, then you can drop more pints which will in essence create a waypoint. Your route will then be calculated with all the pins positions in mind.
Here is an example: