When it's over, check the margin and note the reading. To set the master fader for the highest possible level short of distortion, first reset the margin indicators, then play the tune through from start to finish.
The more old-school approach is to take each tune, master it, then as a separate operation assemble all the tunes into a cohesive whole. As for trimming the starts and ends of tracks, with some music you may decide it's better to have a little room noise between cuts rather than dead silence, or to leave a few milliseconds of anticipatory space before the first note to avoid too abrupt a transition from silence to music.
There is another technique which makes a compromise between mastering as you mix and mastering off-line. Mixing involves balancing levels, panning instrument positions in the stereo field, equalizing, compressing, harmonics enhancing, fixing problems, and adding effects like reverb and delay.
Finally, always back up your original mixed files prior to mastering. If you visit a mastering studio, you might be surprised by just how Spartan most of them are.