To modify which mods are loaded you may need to update the mods= part of the txt file, I havent worked on this for a while but it should be the 1 file you directly modify in the guide.

Hi Mate, got this set up this evening and all seems to be working well. If I wanted to download/remove some mods, how easy is it? Is it as simple as the usual subscribe and add or do I need to go back into the 'servername' folder and amend the line of mods? Thanks