There currently isn't a way to acquire more missles. I thought about having the buildings drop them, and having the dropped missles tween to your ship, but I had a few people play test it and no one mentioned running out of missles. Bit of an oversight I suppose... oops xD
The spatial awareness is an issue I ran into personally. It can be difficult to reorient yourself. I thought about adding a 3D map in the cockpit. However I didn't account for that in my original time budget. I maybe could of pulled it off, but instead spent the extra unallocated time polishing up some things. Next time I'll consider game play over polish, should a similar situation present itself.
Thank you for your feedback. It's extremely valuable in learning to develop quality games!