In Sequence 6, after you do the first naval mission, there is a book next to the Captain. You do your upgrades there. I read you can do them at any harbormaster, but I haven't tried. --- EMPTY [IIIII-----] FULL The WTF!?-o-meter is currently... Normal
Yep any harbormaster at the book. I suggest this before doing most of the naval missions as it makes them much easier. There are some that are really hard (almost impossible) to get 100% synch on even with all upgrades so you want all the help you can get.