For the JIRA add-on, it is possible already. Please create JIRA_HOME/data/eazybi/custom/layouts and JIRA_HOME/data/eazybi/custom/javascripts folders as described here: User interface customization.
Create a file JIRA_HOME/data/eazybi/custom/layouts/_custom_head.html.haml and add link to the custom javascript file colors.js:
= custom_javascript_include 'colors'
Then create new file JIRA_HOME/data/eazybi/custom/javascripts/colors.js. Put this scrips inside new file:
Eazy.Colors.mainColors = ['#4572A7', '#AA4643', '#89A54E', '#80699B', '#3D96AE', '#DB843D', '#92A8CD', '#A47D7C', '#B5CA92','#DA8D98', '#81CEE4', '#DBC63D'];
Highcharts.setOptions({colors: Eazy.Colors.chartColors(36)});
Please replace color codes with your own and you will get your own customized color palette inside your eazyBI