How do you deal with existing files when manually installing mods?

[HeyThisIsntFallout]

I'm manually installing some mods after doing a fresh install of KSP and deleting every mod I had. My game was crashing a lot and I want this to be cleaner and I want to get more efficient with modding.

So, right now, I am manually installing a mod and I am seeing that some files from that mod's GameData file already exist in my KSP GameData folder. For example, I was manually installing Ven's texture revamp and saw that it included Module Manager 2.7.2 while I already previously had MM 2.8 installed. I was told to not add the 2.7 because Ven's will work with 2.8 but KSP 1.3 won't like 2.7. Good advice.

Now, I am installing USI MKS and am seeing that a lot files in the Mod GameData folder that I either already have or in some cases have a more complete set of. For example, USI MKS comes with the Firespitter plugins, but I already have the Firespitter file and it has a lot more than plugins, in it. 

Question is, is there a streamlined way of doing this or is that exactly the work that CKAN was made to alleviate?  Is this a part of manually modding; going through these files individually? Because I'm not sure blindly moving over GameData folders and duplicating files are a stable way to play a game, not to mention, it leads to clutter which leads to the urge to clean install, sometimes. 

A more serious question would be, if i'm dealing with these duplicate files, how do you decide which to keep? My logic would say that if it's already been installed through CKAN, it's probably the newest version.... maybe.

Edited June 2, 2017 by ItsSeanBroleson

[GonDragon]

Well, the first thing should be actually know what are you installing. Some mods has dependencies, that means, they NEED another specifical mod to work. Some others, go a step further, and not only tell you that they need another mod to work, but also they Bundle that dependencie with the mod.

So, when you download a mod to install it manually, there is a posibility that you are, really, installing more than just one mod. At this point, you should think "Why there are so many folders in this mod, and why do I need them?". If you took a briefly look at them, probably you can recognize that every folder belongs to an individual mod, and only one folder contains the mod that you actually are trying to install.

So, What to do?. First of all, read carefully the thread where you downloaded the mod. Some mods overwrite files of other mods for compatibility; All the mods that do such things, advice you about in his thread or in a README file. Second, check those folders, what mods do you have right now; It's more probably that a mod that comes bundled was outdated, than a mod that you installed by yourself. Third, install only what you need; If you already have the dependencies, and nothing should be overwrited for compatibilities purposes, install just the actual folder of the mod.