I'm not sure about wineskin on Macs but Wine on Linux keeps the Windows file-systems in $HOME/.wine/drive_X where X is the Windows-style drive letter and $HOME is your home directory, usually /home/<user-name>.
So, taking an example user-name of "fred", I would take a guess at the mod directory being
/home/fred/.wine/drive_c/Users/fred/My Documents/My Games/Ironclad Games/Sins of a Solar Empire Rebellion/Mods-Rebellion v1.52