The ATLAS level-1 endcap muon trigger system consists of about 4000 Thin Gap Chambers (TGC) with 320,000 input electronics channels in order to find level-1 trigger candidates for muons in both endcap regions. Three TGC stations are deployed with about lm interval with 15m apart from the interaction point in z-direction on each endcap side and the radius of the station (disc form) is about 25m. Usually hit signals are not timely aligned because of different cable length and different time of muon flight. In order to supply reliable level-1 endcap trigger signals, we must adjust timing of hit signals for all the channels with the precision of 2.5ns. In the meantime we have to adjust also the bunch crossing phase used in the TGC system with one from LHC. We need, however, actual bunch crossing signals in order to accomplish this. In this paper we discuss strategies for timing alignment of individual channels with the timing adjustment facility embedded in the TGC electronics system and for the adjustment of the phase shift of the bunch crossing signals.