As of September 2020, the plan was for Starship to install three sea-level Raptors and three vacuum Raptors.
The vacuum engines will likely be used by themselves for the trans-Martian burn from Earth orbit, and the return burn from Mars to Earth, as efficiency matters much more than total thrust for those maneuvers.
Mars's atmosphere is thin enough that vacuum-optimized Raptors would work very well all the way down to the surface, but I would guess for the final touchdown they'll use the sea-level optimized Raptors. That way, only one set of engines will need powerful gimbals with a broad angle range; the vacuum Raptors could get away with lighter-weight gimbal hardware (or even none at all, using differential throttle for steering trim). For the brief landing burn, the loss of efficiency in using sea-level engines should be acceptable.
I don't know if they will use all six engines for Mars liftoff (but my guess is that they will, at least for the early part of ascent); it's a tradeoff between reaching orbit faster to minimize gravity losses, versus getting the most thrust per kilogram of propellant.
The three sea-level engines will be used for Earth landing, as the recent series of test flights have done.