It's all done in the career screen you get when not on missions. Should look like an office.
There's various things in the room you mouse over and click on to save,load, go on new mission,etc.
Save is book on left, can also be done when at see in ESC menu.
Picture of crew on desk is initially for hiring crew but there's tabs that let you "buy" reloads and equipment with rep as well.
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