@Paul_Russo The first thing I had to do was take apart the make file from the Arduino IDE to work out all the switch settings for the various stages. And then compiled all the libraries into Studio libraries for each target processor I used, ready to link together from projects. This takes a huge amount of time and is prone to many issues, Since then I changed my approach.
However, there is now a installable module that appears very popular that emulates the Arduino IDE inside Studio. Personally, I have not tried it, but will give it a go on a new project when one comes along. This is called: “Arduino Ide for Atmel Studio 6.1 & 6,2”. Its free, like Studio. You need an account at Atmel to download Studio and its updates and add-ons, but there is no charge and they don’t appear to spam you.
Next rather than compiling the libraries for each processor, I maintained directories holding all the source code for libraries I used (either Arduino, third party or my own) and these were linked into projects to be compiled specifically. However, if a library was updated for whatever reason, the code for a project, when re-compiled would not produce the same programming code. Rubbish for revision control.
So I shifted to keeping the relevant libraries as sub-projects of each project. Thus if I go back to a project after 6 months and libraries have changed, I have the option of updating the sources or leaving them as they were when I originally compiled them. Makes the projects larger, but revision control is maintained. With the better dependancy handling in Studio, the compiling process is a breeze. Because once a library has been compiled, it rarely needs compiling again as I change the project code.
The biggest bind is actually downloading your compiled code to the target board. This has to be done outside of Studio (or with home made commands in the tools section) as Studio does not support the Arduino boot loader or AVRDude. I use many different programmers: including the Arduino boot loader, but also the Dragon AVR because it supports real time debugging and a couple of other programmers, including using Ethernet boot loaders (very useful for remote networked projects). I use Megunolink to supplement Studio and give me the download and serial interfaces that are missing from Studio. It also has a load of useful other stuff built in. One nice feature is it can watch the HEX file being updated by Studio and it will automatically download it for you, each time you re-compile.
Specifically for FastLED, once you have Studio producing Arduino code reliably. Then FastLED should not be a problem. There are two key points. First is to make sure the compiler version is the same as the one in the Arduino IDE. You can point Studio to use the Arduino version quite easily and then you know you are safe. I actually have a repository of AVR tools with loads of different versions that Studio can use on a project by project basis. This helps me with my revision control too, in case a tool is updated. The next key point is to ensure the compiler optimisation matches that of the Arduino IDE too. Otherwise all kinds of weird sh*t happens. Also FastLED does not compile for every processor supported by Studio, only a very small set, due to optimised code.
Hope this gives you some pointers. I’m not going to give step by step instructions. It would take for ever to write. If you get stuck, do shout.