Integrating Not2Order templates logic into a custom theme can be quite tedious, especially for custom themes.
Because there are many custom themes developed by different companies and individuals no custom theme is the same. Therfore integrating Not2Order logic into such a theme is almost everytime unique for the local Magento installation.
Ofcourse there are some guidelines you can follow to make sure all the logic is copied into your custom theme.
1- Make use of the template fallback feature of Magento
By default Not2Order templates are locates in the folder:
..design/frontend/base/default/template/not2order
You can copy the modified custom theme files to:
..design/frontend/[CUSTOM PACKAGE]/[CUSTOM THEME]t/template/not2order
Enable the use of the Not2Order templates and these modified templates will be used.
Also make sure you copy the following file:
..design/frontend/base/default/layout/not2order.xml
You can copy this to:
..design/frontend/[CUSTOM PACKAGE]/[CUSTOM THEME]t/layout/not2order.xml
2 - Editing the custom theme files
Open the Not2Order template files folder and find the according file in your custom theme. You can use the 'template path hints' feature from Magento to find the loaded template file in your custom theme. If the Not2Order template file does not exist in your custom theme package, you can use the Not2Order template file.
Copy the file best suited for integrating into your custom theme to the new location (see point 1) or edit the file directly in your custom theme (we advise to use the theme fallback principle from Magento). Mostly it's the easiest to use the custom theme file as starting point, but sometimes it's easier to use the Not2Order default file as starting point. This choice is completely up to you.
Now comes the hard part, what goes where? You need to figure out where the Not2Order logic goes into your custom theme file. This is different for every custom theme. The changes made for Not2Order to the default Magento theme (..design/frontend/default/default/template) are mostly commented with comment tags (// for PHP or <!-- --> for html) The code behind the comment is the modified Not2Order code you need to copy to your custom theme file.
This has to be done for all the Not2Order template files compared to the according custom theme file.