I have done that several times, and I would like to clarify, it says to install Adv Recon Trap Detection, then to install nightvision patch and DLC patch and click merge. What I took that to mean is install the first file, then install the other two with the same name and click merge every time the option comes up. Is this what I should be doing?
UPDATE: I just decided to go into window explorer and manually drag from the overwrite folder and it worked. Will this cause any problems as I didn't do this through the mod organiser?