There's quite a lot to unpack here. The yaml.jsf are all at the top of the file; "white" isn't listed anywhere, and the only mention of "green" is for comments. My guess is that you have a terminal palette that's something other than black text on a white background. In that case, your emulator is mapping the specified colors to something else in its palette. You'll have to work out what that mapping is, but at the very lease we can say it maps cyan (i.e. "Constant") to green.
As for editing .jsf files: There are two location ne will look for .jsf files. First it'll look in your ~/.ne/syntax directory, and if it finds ~/.ne/syntax/yaml.jsf, it will use that. If not, it will look in either /usr/share/ne/syntax or /usr/local/share/ne/syntax (depends on options your ne was built with) and use the appropriate .jsf file it finds there.
However, just changing the file isn't enough; ne only loads any given .jsf file once and caches it in memory, because they don't normally change. If you are actively working on a .jsf file and you want to see the results, you need to fire up another instance of ne to get your changes loaded into it.
When I'm doing work on a .jsf, I have two terminals open: one with an ne that has my ~/.ne/syntax/<whatever>.jsf open for editing, and the other for starting another ne with a sample document to test the .jsf I've been working on. Any time I make changes to the .jsf, it's necessary to quit the sample ne and start it back up again to be sure to load the latest version of my .jsf.
Once I'm done, I usually throw it away because it's rubbish. But on the off chance I actually did something right, I'll leave it in my ~/.ne/syntax directory if it's only of interest to me, or I'll move it to /usr/share/ne/syntax. If it's really good, I'll consider making a pull request to ne's github repo and/or the https://github.com/cmur2/joe-syntax
project from which ne gets most of its .jsf files.
I hope that helps.