problem 1: i appear to have two mod-entrenchment v1.051 files. One has two folders i reckognize these two being mods i downloaded. The other does not.

Problem two: i recently downloaded the malestrom mod (found on moddb.com) and once iv saved the folder and extracted it to the mod file i noticed that it isnt one folder, its about 10 folders each with stuff like mesh, game info, etc. its almost as if  the main file holding this all was deleted and all that was inside is now spread out in my mod file. what should i do? should i make another file and put all these files within it?