combine the quartus projects

hmm... here my situation is that 2 engineers were designing a project. i was makiing internal part (processing etc,) and my co worker was doing interfacing with surrounding chips. now we have our own projects own pin assignments (of cource they are in seperate banks.) if ill make my procet's symbol and he'l make he's; yes we may put these two symbols side by syde and connect them but which one will be the top level project? and how about 200 pins on each side? these pins now remain inside

in these projects... if we will get these pins on top level this creates hundreds of other problems. any solutions... ? im sure there is some way, people all around the world make huge projects each of them is devided across tens of engineers, there must be some way they link their work.