Hi mate i will try to provide some answers and if i get em wrong i'm sure someone like cobra will correct it for me.
1) Which tool am I supposed to use for mapping: the MOHAATools package, or the Spearhead SDK? I am hoping to create my map more for MOHAA and BT, not so much for SH (although it would be nice if it worked in there too).
Answer is mohaa tools for maps for AA only and SH SDK for your BT maps
This is simply so you dont have to start changing stuff in the preferences each time. So set the SH SDK mod dir to maintt instead of mainta to access BT specific stuff.
2) I'm having some strange problems with my entities list (the one that appears on the menu when you right-click in 2D view). Many of the entities appear twice on the list, whereas others don't appear at all (I know they should be on the list, because Radiant on my brother's computer has more entities on the list).
You need to have the ent defs file in the right place so it sounds like there are 2 versions in the one place so it is reading it twice.
3) I'm not so sure about this, but I believe that I am missing some textures as well.
You may well be but check your settings as it maybe set to just look in main for example also do you have a little arrow at the bottom of the texture list clicking this will scroll thru the other textures you have.
4) Why does it seem that the entities list that appears when you push "n" has a lot more entities than the list when you right-click in 2D view? Is it just because the list that appears when you push "n" includes all entities in the sub-menus of the other list as well?
Thats right it shows prpoerties (as far as i know) for all entities you have access to.
At the end of the day it all boils down to how you have it set up.
here is a site a lot of us have found very useful.
http://users.1st.net/kimberly/tutorial/ ... ingmoh.htm
Lastly good luck
Scorp