The 3 vacuum engines will be used for Trans Mars Injection (TMI) since they are more efficient in vacuum. While each one is off centered, firing all 3 will make it balanced, so this makes the most sense.
For landing, it will be a bit trickier. I haven't seen anything publicly, but I suspect they will use the vacuum engines for part of the time, and the 3 sea level engines for the final landing. The 3 sea level engines will give maximum flexibility for the most critical point, but the vacuum engines can be used for parts of the decent if required. The sea level engines are more central, and can gimble, allowing for this flexibility.