A dedicated channel is planned, but meanwhile by using the Normal channel and some brush parameter it is possible to paint flow maps in Substance Painter.
Step 1 : Create the normal map
Create a normal map texture of 16 by 16 pixels. The color has to be 128, 255, 128 which should give the following color :
(This color is the equivalent of a vector looking up, in DirectX)
Step 2 : Add normal channel
In your Substance Painter project, add a Normal channel via the texture set settings if this channel doesn't already exist.
Step 3 : Setup of the brush
Enable the follow path feature in the brush parameters. Load the normal map texture (step 1) into the normal channel slot. Disable the other channels.
Step 4 : Paint !
By painting on the mesh with the follow path setting enabled, the brush strokes will draw directions into the normal map.