Alright here's my second post.
Firstly, I would like to thank everybody who gave me such good ideas in the previous discussion. I'm working on getting all the mods that were suggested and also opening up a thread where I'll tell about my journey. Sadly, progress has been halted and this post should clear up why.
Anyway, I've started creating my mudpack with all the good mods and then a few I found. I started with Kerbal Atomics, mainly because it was small and useful, but also because I like the mods and features. So I moved the Game Data folder into the correct position, and started up KSP. When I got there, none of the actual mod items were there, but it was still giving me options to use things such as Liquid Hydrogen and other subtypes. So this raises my question: what am I doing wrong? I've got all the mod setup correctly and got all the essential plugins, but it just won't give me the items. Please help.