I keep running into damp stones every where. Is there a way to get through them, or do I have to make a separate cave for them? Also, can I use them to make mud? I still haven't quite figured out farming. Or hunting for that matter...
You can dig through damp stone, if you know what you're doing (don't accidentally break into a river without proper precautions! but going under a pond is ok). What you have to do is designate the square again.
Aquifers are another matter entirely. Take a look at the wiki on how to deal with them - I have been scared of them and avoid them on embark.
You can't make mud from damp stone, for that you need to let water flow over ground. Also see the wiki.
Post your other questions as separate ones, and I'll see what I can do :-)