ok for mkflat....heres what I did.
Create modfolder under users, create my_addon in modfolder. Create !flatlist in notepad (or modify that file from unflat) and save with files in modfolders (NOT MY_addon). Heres where I went crazy for 8 hours. Just forget about mkflat .cmd file. Heres the easy way.
Open notepade and save this as mymkflat.cmd (or whatever really).
starter.exe root\programs\mkflat.progpack, users\modwork\my_addon.flatdata, users\modwork\my_addon.!flatlist
Thats what I did and it works for me. I went wrong thinking that mkflat.cmd file was set up like it was calling for in the manuel. When I finally opened it up in notepad, was like oh duh. Happy flattening.