[polyfractal]

Well, there are both retrograde and anterograde tracers. So you can trace from either target->source or source->target depending on your choice of tracer.

These tracers are used to map circuits because they are passed from one neuron to the next via functional synapses...which means that any neuron that is stained must have been in contact with a previous neuron, etc etc.

The "connectome" is built up by injecting a limited amount of tracer in a single region, in multiple animals, to provide a mapping of that region. To get the entire brain you need lots and lots of injections in a very large number of mice (and a lot of technicians slaving away over cryostats).

To your point about not labeling synapses and gap junctions: those are relatively unimportant when considering wiring diagrams of the brain. What is more important is knowing which partners a neuron synapses onto. You don't really care how many synapses are involved unless you are looking at single or clusters of neurons, nor can you really measure it without some other method (e.g. electrophysiology).

Caveat about tracers which often goes unannounced: the staining of a tracer in a secondary neuron is only as strong as the connection between the primary and the secondary. Which means that a neuron who synapses strongly will be much brighter than a neuron that synapses weakly. Similarly, tertiary (and quaternary, etc) neurons become progressively weaker stained as the exponential dilution of the tracer kicks in.