Each syntax can name their own scopes, but they are based off of this list. For instance your syntax might specify that function
is storage.type.function.js
scope. If your theme supports that directly it will use that color, otherwise it will fallback to storage.type.function
then storage.type
then finally storage
trying to find a color in your theme.
Since you are creating your own style, I would recommend installing ScopeStatus (CTRL+SHIFT+P, then Install Package, then ScopeStatus). Looking at a file using the syntax you want to concentrate on, do CTRL+SHIFT+P, then "Scope: Show in Status Bar". Now you can move the cursor to various elements to see what scope they give and you can use those to define colors.
You can check your themes to see what they do, go to "Preferences->Browse Packages" to open the folder where your packages are stored. I installed "Theme - Phoenix" which has a folder and a "Color Scheme" folder underneath. In one of the theme files I found 16 colors that were used for various scopes:
keyword.operator.class, constant.other, source.php.embedded.line
variable, support.other.variable, string.other.link, entity.name.tag, entity.other.attribute-name, meta.tag, declaration.tag
constant.numeric, constant.language, support.constant, constant.character, variable.parameter, punctuation.section.embedded, keyword.other.unit
entity.name.class, entity.name.type.class, support.type, support.class
string, constant.other.symbol, entity.other.inherited-class, markup.heading
keyword.operator, constant.other.color
entity.name.function, meta.function-call, support.function, keyword.other.special-method, meta.block-level
keyword, storage, storage.type, entity.name.tag.css
invalid
meta.separator
invalid.deprecated
markup.inserted.diff, markup.deleted.diff, meta.diff.header.to-file, meta.diff.header.from-file
markup.inserted.diff, meta.diff.header.to-file
markup.deleted.diff, meta.diff.header.from-file
meta.diff.header.from-file, meta.diff.header.to-file
meta.diff.range
Different themes might have different settings, for keyword.operator.class in the first group might have its own color or be the same as meta.diff.range.