All three tiles link the layers you selected and make a new Synapse layer. They differ in which pairs get a line. Hover a tile before you click and the sky previews its lines.
Chain: one after another
Chain draws a line from each layer to the next, in the order you selected them. Five layers give four lines.
Use it for a path through points: a route on a map, a snake of shapes, the wing of a constellation.
Selection order is what counts, not stacking order in the timeline, so select the layers one at a time in the order you want.
Hub: out from the first
Hub draws a line from the first layer you selected to every other layer. Five layers give four lines, all starting at the first.
Use it for a center with spokes: a team around a person, a logo with satellites, a tail fanning from a body.
Web: whatever is close
Web links every pair of layers closer than Max Distance, 300 px by default. Each line fades out over its last 100 px of reach and is gone past it.
The caption counts the lines in reach right now out of every pair, here 14 of 66 lines in reach.
Web stores a line for every pair, so as your layers move, lines join when two layers come close and let go when they drift apart. That’s the plexus look. The sky and the tile’s count show only the lines in reach at the current time.
Web links up to 40 layers. With more selected, the tile says Max 40 and nothing changes.
Set the starting Max Distance in Synapse’s settings, or change it later on the Synapse effect along with Fade Distance. Style and animate the lines shows how.
A plain click always makes a new Synapse
Each tile click makes a new Synapse layer from the layers you selected, even when a Synapse is selected too. The selected Synapse stays as it is. To put more lines into an existing Synapse, Shift-click the tile instead, as described in Add lines to a Synapse.
If a Synapse in the comp already has exactly the lines you’re about to make, the tile says Linked and Synapse doesn’t make a copy.