there are 3 things that i can point..
first one would be
Install Part1, Part2 and the 6.1 Patchinto the default Medievall II Total War directory.
Normally this is: .../SEGA/Medieval II Total War.
If you have installed Medieval II into another folder, please select the folder manually.
NOTE: Stainless Steel 6.0 will not overwrite older Stainless Steel versions, so you have to delete them manually.
not in mods.. as that way it probably creates loops of folders.. which it shouldnt
second if its steam version
steam games comes in for you would be x:\program files\steam\steamapps\common
third ss mod have its own launcher.. use that
last but not the least.. get 6.1 and 6.2 patches..