creating your own template is straight forward process which I'll describe in a few steps:
1. Copy the /App_Themes/Default
to your own theme name (e.g. /App_Themes/YourThemeName
2. Now you should copy or create your own Master pages that inherits from MonoX.master
(We recommend that you copy your Master page to the /YourAppNameFolder/MasterPages/YourMasterPage.master
3. Change your Master page layout as you like (Header, Content and Footer sections) - for more information take a look at the Master pages
and Nested Master pages
4. Change the CSS from the Theme folder to suite your needs and to follow your Master page layout design
5. Decide which MonoX built-in modules you need for your Application / Web Site and then approach to redesigning them (You can find all MonoX built-in module templates at /App_Templates/YoutThemeName
6. More on Page and Module templating you can find in MonoX manual under the section "14.6 Themes, templates and chromes"
At the moment we are performing some optimization tasks related to whole MonoX mark-up (Master pages, Pages, Modules, Module templates) and CSS so our users can easily copy or change the block of design that they need. If you are not in the rush and you can wait a little bit more we are planning to release new version of MonoX at the end of the next week with all these changes (We need a few more revisions to fix some styling issues) ? Shortly after we release new version we will provide the community with the detailed walk through on how to create a custom design.
You also can find more information in these posts:
How to: Create a custom pager template
Building a custom Web part