Automatic Z/Y flight rule changes
Eurocontrol maintain a database about the permitted operations at each airfield, i.e. whether VFR/IFR departures and arrivals are possible. Autorouter automatically generates Zulu (VFR departure) and Yankee (VFR arrival) flight plans, where a Z flightplan can also include a VFR arrival based on what is stored in the database.
Whenever possible, autorouter will choose IFR procedures assuming this is what you want. If you have an Enroute Instrument Rating (E-IR), i.e. a rating that only allows you to fly IFR enroute but not instrument departures and arrivals, there is a checkbox in the user profile settings. If this is activated, autorouter will default to VFR departures and arrivals.
Manual flight rule overrides
In some cases, you might want to override the behavior and choose a VFR departure or arrival by setting one of the checkboxes. In some countries, IFR departures are permitted from all aerodromes (e.g. UK or Denmark) but in reality you often want to do a Z departure and sort out the clearance in flight.
Selection of pickup/IFR cancel waypoints
The goal of the router is to minimize your VFR legs, assuming you want to be IFR for as much of the flight as possible. In some situations you might want to influence the pickup/cancel waypoint. In this case you open the SID/STAR section (which is called “Pickup” and “VFR change” respectively when a VFR departure/destination is selected) and enter the name of a waypoint or navaid.
There is another angle to this: when on an IFR departure/arrival, autorouter has to take the performance characteristics of your aircraft into account. All legs are to be flown straight and only climbs and descents are generated that are within the aircraft’s performance model. Assume that an IFR route would start at a VOR very close to the airport but a restriction requires you to be at FL100 over the navaid. An IFR departure will not be able to directly go to the VOR because the short distance will not allow you to climb to FL100. Instead, autorouter will choose a more indirect route that allows you to stay within the envelope. If you choose VFR departure instead, autorouter will disregard climb performance (assuming that under VFR, you are not bound to flying a straight leg and can somehow gain altitude) and perform the flight rule change at the adjacent waypoint.