the artifacts are for upgrading items at memory alpha, there is a store there that lists what you need to upgrade x item to y item.
there is a button at the bottom of your mini-map buttons shapped like a down arrow, one of the options there is to go to your bridge, atm you can't do much other then walk around your bridge, but in the future they said they would develop more for it, if its something we want to do. so the different options in the customization, just determine how your bridge looks.
oh and a new ship every promotion. LT, LtC, Com, Capt, Admiral