I have a problem with underground river critters... How can I dispose of them? They are of the skeletal sort.
I can't close in to melee, because the upper level is just air and the lower level is full of water, right? (UR channel is made of 2 z levels, one is water one is above water)
I can't kill them with crossbows, as they are skeletals?
You can kill skeletons with crossbows, it's just not very easy. Basically, do your best to arrange it so that your marksdwarves use only low-value bolts, like bone, since you'll probably not be recovering them for a while or ever, and just unload many, many bolts at the skeles. Most shots will just glance off with little to no effect, but some will actually hit and break bones and eventually kill the undead freaks.
Or, as an alternative, you can dig out a little platform on the riverside next to the open level. Aquatic creatures can climb out of the water to the level above if there's a place for them to, so if you clear such a space the undead will come to where you can melee them. This is much more dangerous, however, since your melee dwarves might stupidly dodge into the river or jump in to attack; either way, they are likely to drown.
My woodcrafter stops working when ever I tell him to make wooden cages. If I delete the cages and add other things he will make them. When ever a cage is the next thing, he stops.
Any ideas?
You mean a carpenter, not a woodcrafter, right? Wood cages are made by a carpenter at a carpenter's workshop, not by woodcrafters at a craftsdwarf's shop. I don't know of anything that would make a carpenter not make cages, but if you're trying to designate them through the manager and you've only got a woodcrafter, you simply don't have the right labor.
Otherwise, no idea
And is there some problem with magna smelters making pig iron. Lots of iron smelted, and lots of flux(whole floor covered with it) but no pig iron option.
As Diablous said, you need charcoal or coke for pig iron, and also steel. This means that for making steel bars, magma smelters don't actually have any benefit over normal smelters; you need 2 fuel, 2 flux, and 2 iron for every 2 steel whether you're running the reactions in a magma smelter or a non-magma smelter.