i have been to scared to even try this before but can i leave the cockpit and go to another room without having any ship problems like aborting hyperspace etc.?
Yes, to a degree. When doing any travelling, you can move from room to room in the same entity without causing any problems. However, if you try to board a docked entity (ie a vehicle in a ship) this will cause travel to be aborted. The only way to prevent this is to have a droid with the correct piloting skills (R1 for capital ships etc) assigned to you, and in the cockpit - this will prevent travel abort.