Use the screen between your knees to summon your ship. The count down will let you know when it should arrive near to you.
If you are in a settlement and have your ship docked; request docking and follow the dot on your compass. This will lead you to your ship or the garage you need to be in to embark your vessel. You can tell you are in position in the garage or under your ship as the "board ship" indicator (where the mass lock indicator normally is on the ships hud, under the fuel consumption rate) will light up.
