PF3 first checks for arriving and departing AI traffic and will use the same runway the AI aircraft are using. If no AI are detected, PF3 makes an initial runway assignment based on wind, then periodically rechecks for AI activity. If AI are later detected using a different runway, you may be issued a runway change to match the AI.
You can control which runways PF3 will assign to YOU for takeoffs and landings. Click the SIDs/STARs button, type the airport's ICAO code, and press Enter. On the airport runway list, you can designate (at left) whether each runway is to be used for takeoff only (T), landing only (L), both (B, the default) or closed entirely (X). If for example there is a 27L and 27R, and you want to land on 27L when the airport is landing to the west, designate 27R as either takeoff only (T) or closed (X). Remember that these preferences apply only to the runways PF3 will assign to you, and do not apply to AI traffic.