@hemebond Hrm. So you press 'R' (gamepad X) to bring up the scanning tool, and with certain objects pressing it again will let you connect and interact with them. There are supposed to be on-screen prompts for this stuff, especially during the tutorial. I'll have to double check if I missed that one...
edit: Oooh. So now that I've had time to review this better. You would have already seen the scan/interact mechanic I guess. After collecting the materials you don't have to "dock" with the skiff, you just activate it again with the scanner to open it's UI. Is that your confusion? How would you suggest making that more clear?