You should not start with bootstrap in that case. I think especially in the beginning when you are learning CSS you should build something from scratch. Otherwise you have to learn both, CSS and how bootstrap is constructed.
CSS is not hard. I don't consider myself good at css, not at all, but give me a mockup and I can reproduce it, with a lot of Googling and trail-and-error. At least for me, though, what is really difficult is to make something from scratch without a mockup. It might be because I am not much of a visual thinker. I am a coder after all, not a designer. A professional designer might already have this mockup in her head. I don't.
So what I need to do is create the mockup in Photoshop first. There I can experiment, move stuff around, change colors, shadows, etc. When I am done, I reproduce it in css. I guess when you are either a very strong visual thinker or you are already very good at css, you don't need Photoshop. Otherwise I recommend you start with a mockup and then make a pixel-by-pixel reproduction of it. That way you can solely focus on the How, not the What. If you do that it's not hard at all, and you don't need a code academy for it. [That said I like the idea of a code academy for building a website from scratch for non-coders]