I'm actually well on too my way towards making the bio layer. I even have a plan for making the entire layer (that is too say, all 100 squares of embarkment space) into it. Note: It is right below the lowest surface layer, so that is exactly 100 squares of embarkment space.
Since the bio layer has 3 parts, the space between the trees and the cieling, the actual muddy layer, and then the ground floor which contains the river.
Now, here's the awesome part. Before channeling out the floor between the topmost z-level of the bio layer and the middle layer, you can make it into a grid of holes :3 once this is done, you turn all the holes into ponds, and have them be auto filled. Water will be constantly poured into these layers and thus, the ground muddied =D It'll take a long time, but it'll eventually muddy the entire z-level :3
The alternative is a network of screw pumps.
Once I'm done with the bio layer, I'll begin carving out the interior of all the towers, and abandoning the surface fortress. Once complete, I'll begin actually creating the abyss layer. The lowest z-level will be left free for a while. But I'll begin emptying the magma pipe into it slowly, this way it'll slowly fill up as I expand it over the ENTIRE z-level :3 no magma evaporation.
edit: When I've done. I'm gonna save scum and make an abandoned version. Then post it for everyone to go and reclaim and or explore with their adventurers. The artifacts will be placed in a secure vault deep in one of the peripheral towers, probably with a bunch of coins too, and the tombs of the kings and such. Everything else will be destroyed or deconstructed. Leaving only the skeleton of the fortress for you guys to play around with as you will.