In synaptic vesicle fusion, the vesicle must be within a few nanometers of the target membrane for the fusion process to begin.  This closeness allows the cell membrane and the vesicle to exchange lipids which is mediated by certain proteins which remove water that comes between the forming junction.  Once the vesicle is in position it must wait until Ca enters the cell by the propagation of an action potential to the presynaptic membrane.  Ca binds to specific proteins, one of which is Synaptotagmin, in neurons which triggers the complete fusion of the vesicle with the target membrane.
SNARE proteins are also thought to help mediate which membrane is the target of which vesicle.