Flagging a route lifts the route up to the first place in the route list. This is mainly so that you can easily keep an eye on a specific route, if you need to.
When you preschedule, you are required to hire the staff for the aircraft immediately. I suppose it reflects the reality that staff has to be trained before they can actually do the job. If you want to save on salaries, there's no other way than to schedule the route as late as possible.
If you don't hire all the required staff, you will get cancellations. So, this is not a bug, but a feature.
When you lease an aircraft, you pay for 4 month's lease. In other words, after that payment, you only start to pay for the aircraft's lease after 4 months. So it's exactly as you said.
Hope this helps,