AS3 is the same, no matter the IDE.
The main difference between CS and FD is that CS is animation software, and thus, it’s more suitable for animators than for programmers. ie, it has horrible debugging capabilities, slow compiling, creates huge files for no good reason, you have to mess with the settings to be able to use Flex, etc, etc.
On the other hand, it’s very newbie-friendly, including a drag and drop interface, a graphics editor and stuff like that; it looks more like Paint than like something a programmer would use.
The other, programming-oriented IDEs lack all of that fancy stuff; they’re text editors (with great options like auto formatting, code completition, bracket pairs or syntax highlighting) with a compiler. You do everything with code.
When following a CS tutorial, it’s pretty much the same, the main difference is that when they say “drag your image to the white area”, instead you will type a single line to include your graphic, sound, video, text or whatever.
The other difference could be with tutorials which vomit code all over the timeline, but instead of implementing that with code, you should simply close that site and avoid it like the plague, as you’ll get nothing but bad habits from someone who does such things.
And… about Flixel. My personal opinion is don’t use an external library, engine or framework unless you already understand the language and what the framework does. The hows and whys.
Good: I know how to do it, but I’m too lazy to write the whole thing, so I’ll just go and use X library.
Bad: I don’t know how to do this, so I’ll just use someone else’s code.
For a tplace to start, try this. It’s not perfect, but it’s better than most of the AS3 newbie tutorials you’ll find out there.