"is there anything particularly heinous with subtract and merge"
When you do a CSG Subtract, look to see how many fragments are made because each fragment basicly equals one brush.
CSG Merge can be your best friend because it takes 2 brushes and turns them into one.
"you can just put in models somehow? "
Yes you can make models in Gmax( free version of 3d studio max) and export them into quake 3. I have just started to pick this up myself and am makeing some good progress.
""light effects" like flare"
Flares can be really simple to make it is just a 2d image with autosprite on.
I put the new in b.