Welcome to the Wing Commander section of CIC Game Guides.
The success / failure outcomes at the end of each series is based on your performance throughout that series, not just how you perform on that last mission. If you are unsure which system you are in, go to your locker.
The mission branching means that you won't fly every mission or go to every system in the game in one run.
You may sometimes need to manually select Nav points which is done by clicking the point in your Nav map which is accessed by pressing the N key.