Can I merge two ceiling light fixtures into one with two wall switches?
Can I merge two ceiling light fixtures into one with two wall
  switches?


To answer your first question, yes.  Almost all light fixtures have a white and black  wire for each individual socket.  Simply send one to each switch.


  Do I just make one of the wall switches a three-way?


Well you will need a "traveler" (extra wire) between the switches for a 3-way.  There are a couple of different ways to wire a 3-way here but if your walls are closed and you don't want to open them then the answer is, no.