I don't know how to program for the Atari, and I wrote the music for one of the homebrew games on this site. I used Capella, which you can download for free from here. They have other platforms if you don't have Windows, too. This program has a built in "mouse piano," that allows you to just click on the notes to transcribe them (assuming you can read music!). I've tried a lot of different notation programs, and this seems the most complete.
Although it's a demo version, pretty much everything you'd want to use is accessible, except you can't use the lyrics function (which you probably won't need for Atari music, as far as I know), and you also can only have up to two tracks per system (which was also not a big deal for me when writing for the Atari). There's a bunch of built-in voices, where most instrumental sounds are represented. I don't know about creating "noises" or other Atari-esque sounds, but it's nonetheless very easy to use for the most part.
If you want to look at a screenshot, there's a link on the download page.
Hope that helps!
Good luck!