For each mod it is recommended to have a separate installation folder. This is because the mods overwrite the same files, so changes from other mods/patches overwrite content which in 98% of the cases leads to crashes, glitches, bugs.
Most bloodline players have 1 clean installation folder, right from the scratch. Then copy this folder and install the mod/patch in it. So many, like me, have 4-5 bloodlines folders, each with a different mod/patch installed.