Yes, it matters. The Alda line has to blow out the vent in the top when powered, the manifold shouldn't.
The manifold to lower is how my car is plumbed, I just looked, but it might be wrong (works though). Whichever one blows out the top/vent when you apply 12v to the solenoid is the one to the Alda.
There is a picture here somewhere.
here it is:
http://www.peachparts.com/shopforum/showthread.php?t=183791&highlight=alda
Shows the manifold line on the bottom also.