(The way to remember this is to remember that a dwarf has to stand in the open tile, and on something, to construct the pump.)
My way of dealing with it is that on any level with a pump, it alternates "_+_+", a channel to suck up at one end, a floor to hold water (to be potentially sucked up) at the other, and the channel in the middle (not adjacent to the other channel) is the one for the power transfer.
If I'm digging out of bedrock, I'll often dig the following, with the entrance from the north being temporary for digging and punmp installation:
### ##
#_+_+#
######
(If I'm smoothing the shaft, I leave the left-hand channel until after I've smoothed the walls that can only be accessed from there.)
Then installing the pump ("pumps from west" in this example):
### ##
#_%%+#
######
Then (for a top-powered system) seal it up.
######
#_%%+#
######
(If I'd have had the entryway one to the left it may have caused problems with trapped dwarfs, beyond the 'power channel' and even the pump-head. Depending on other factors, but I don't think I'd have needed to seal it, if I remember right. Though it's a long time since I was so slap-dash about it.)
Then on the level above (note you have problems if you don't make the bottom-most pump first before adding the one above it, before the one above it, etc, but you can start carving it out right from the start, and designate the placement of the new pump before you seal off the level below) you need to head towards:
######
#+%%_#
######
^ channel under here
For a
built tower, then the idea is similar, except that you're placing floors and walls, leaving voids and gaps, rather than cutting openings and channels, leaving walls and floors. And this means masons (or carpenters) running in and out with materials, getting in each others' way, rather than miners that you can usually manage with a little mroe ease.
But trial and error is probably the best way to learn. And to see what I mean (and or
really mean, if I'm not explaining it correctly.
.