Mostly a combination of both.
If I want to examine the current situation, itīs usually the totalizer that is first checked.
For predictions and checking options, the FMS is good enough, but comes with several operational caveats depending on type. One has to have an idea of what goes on inside the box. If it bases its calculations on a performance model, better be sure that this model is appropriate to the present aircraft configuration if You do not want to end up like the Hapag A310 at VIE some years ago. If its calculations are based on current fuel flow and TAS, it will massively underestimate the remaining fuel at destination during climb and only slowly approach realistic values during cruise and descent.
And I also subscribe to Goldenrivetts words. A quick check to see whether fuel on board plus the amount the FMS believes the aircraft to have used is equal to the amount of fuel You found in the tank during the pre-departure fuel check is a good way to spot many malfunctions in the fuel system early (-ish).