I was in the same boat about three years ago when I first started modding. There is always more to learn, even the experts are still making new discoveries. Bethesda gave us a nice CK but they didn't include an instruction manual, so modders have needed to figure out how the CK works by themselves.
The STEP guides Nephenee linked are awesome. I don't follow their step by step instructions for what mods to install because I prefer to build my own load orders, but I have read several of their guides and they are very informative, well written adn they keep them updated pretty well. Plus the STEP folks seem like really nice people.
Okay, let me stop you right there and clarify something. Nexus Mod Manager and LOOT do entirely different things. NMM is a mod manager, where as LOOT is a load order sorter that also includes helpful information about individual mods in your load order.
Your choice of mod manager is important because if you want to switch, you will have to reinstall all your mods and probably want to reinstall the game just to make sure you start with a clean install. So, picking the right one in the beginning is important. The choices are Nexus Mod Manager, Mod Organizer and Wrye Bash.
Nexus Mod Manager seems to be the easiest to learn, ans seems to have been improved from three years ago when I first started. If you just want to install a few mods, it's perfectly fine to use NMM. But if you are planning on becoming a modding "enthusiast" who makes modding a dedicated hobby, you might want to pick Mod Organizer or Wrye Bash.
Mod Organizer is used by STEP and there are many tutorials for how to install individual mods with it. I have always used Wrye Bash, but when SSE comes out, I plan on using Mod Organizer. It has a great profiles feature that lets you easily switch between different mods for different characters. I'd probably recommend it for a beginner because of that and because it is so easy to get help with an installation issue because there are so many active modders using it and so many tutorial videos available on line for Mod Organizer.
I have always used Wrye Bash. Some of Wrye Bash's functions like the bashed patch can be used in conjunction with other mod managers, so you can open Wrye Bash through Mod Organizer, for instance to make a bashed patch. But Wrye Bash is so much more than just a bashed patch maker. It has numerous features for managing installation of mods as well as load order. To many functions to list here. However, its profile feature is more limited than Mod Organizer because Wrye Bash lets you switch between individual load orders, but not individual installation orders, when you switch profiles.
LOOT is a tool you will need. LOOT tells you the optimal order to load your mods. I have gotten to the point where I just sort load order manually by looking at the individual mods in xEDit, but for now you should definitely use LOOT (in conjunction with your mod manager). There are three good choices for a mod manager, but only one LOOT. The old BOSS is outdated for Skyrim (though its still being updated for Oblivion and can be used for that game).
You also need to learn the difference between install order and load order. Load order is the order the game loads the mods when the game is run. Install order is the order you install your mods. Install order does not matter for mods that come with a bsa file (bsa is a proprietary archive file type created by Bethesda that works much like a zip file). But install order is important for mods that come with loose files, since some of those files may "replace" files that come from other mods. (If two files have the same name, only the one that is installed last will have any effect since it will "replace" the earlier installed file).
Load order is important because of the "rule of one". The rule of one is that a single record can only be changed by one mod, and if two or more mods try to change the same record, only the last loaded mod will have any effect in the game on that record. There are some exceptions to the types of records that this rule applies to. Changes to a landscape record for instance will be merged when the game runs. But most records are subject to this rule, which is why load order becomes so important. (Load order is also important for mods that come with a bsa file, since load order will determine which files from those bsa files are used when two bsa files contain individual files with the same name and file path).
You can see the rule of one in action by looking at your load order in xEdit. xEdit is a very powerful tool. Here is a https://www.youtube.com/watch?v=CQi7vnqXyScto an excellent tutorial on some of xEdits more advanced features. It can do a lot more than just automated cleaning.
Good luck and happy modding!