The problem with underground tunnels is that it doesn't sound like you get enough water to keep them filled - which means the water will likely evaporate before reaching a destination.
I have a solution which prevents this, but it requires a little math.
Let's say you have a pool 50 tiles away from your fortress and another 50 tiles beyond that.
If you have water which is consistently 2/7 or deeper and underground, it won't evaporate. If you dig straight down through one of the pools, not through a muddy tile if the pool is small but one tile off of there (with as many murky pool border tiles as possible since only those tiles collect water) or through the center of a larger pool (since you'll have more problem getting water to flow into the channel from a large pool) you can create a tall, narrow local cistern which will quickly reach 2/7 depth and deeper. At the bottom of the local cistern, you dig a horizontal tunnel to move the water towards the fortress (or toward the next pool), with a floodgate separating the local cistern from each tunnel.
How big should the local cistern be? Well, you need to fill the adjoining tunnel (50 long in our case) to 2/7 depth at least. Let's aim for 3/7 just to cover any small math problems and any evaporation while the water works down the tunnel. That's 50x3=150 units of water or 150/7 = 22 full tiles of water. A 2x2x6 tall cistern would work, or a 3x3x3 tall cistern would work. Not too bad.
So, you build a 3x3x3 local cistern under each pool with a 50 tile tunnel connecting the two and another connecting the closest to the fortress. As soon as one local cistern fills to a full 7/7 depth, open the floodgate to let the water into the tunnel leading in the direction of the fortress. The 27*7=189 units of water will spread out over the 50+9=59 tiles leaving about 3/7 water over the entire area. At this point you can leave the floodgate open and any additional water will just fill up the tunnel. When there's enough water to open the cistern system further and keep it at least 2/7 depth, open the next floodgate.
At the fortress, create a larger cistern (that the dwarves can access via well) that can receive this water - deep, but not so wide - but you need to make sure that the large cistern fills at least to 2/7 uniform depth *and* that you don't take so much out of the feed system that it falls below 2/7. You can use the floodgate system to drain a subset of the feeder tunnels (maybe just the last 50 tile tunnel into the large cistern), then close the feeder system off and use other parts of the feeder system (the other 50 tile tunnel and the two local cisterns) to refresh the one you just drained.
For the ambitious dwarfy, this can be pretty easily automated with pressure plates at the 'shallow end' of each tunnel and double floodgates to ensure that one part of the system is ready to deliver and the next ready to receive.
To minimize evaporation in the murky pools, put a hatch cover over the drop down into the local cistern to keep the water there (or it'll never, ever flow from the outer area) and when you're pretty sure the rain is over, or summer is about to hit, open the hatch cover and claim the water.