Ok, got it. First you need to set the processing options for the js file to Embedded Resource Then add it to the AssemblyInfo.cs:
[assembly: WebResource("namespace.filename.js", "text/javascript")]
Then override the GetScriptReferences method in the class that inherits from FieldControl:
public override IEnumerable<ScriptReference> GetScriptReferences()
{
var baseReferences = new List<ScriptReference>(base.GetScriptReferences());
var newRef = new ScriptReference(javascriptPath, this.GetType().Assembly.FullName);
baseReferences.Add(newRef);
return baseReferences;
}