After you set up the profile and mapped the variation values you will need to set the category up for synchronization.
1. Open the module page.
2. Click the "Categories" button.
3. Scroll through the categories, when you find the category containing the products you wish to list on Amazon, click the checkbox in front of that category than from the drop-down on the right, select the profile that you created for this category or a profile that fits this category. You can use the same profile on multiple categories.
Eg: If you have a category for running shoes, for trainers, for fashion shoes, you can use the same profile for all 3 categories.
4. After you finish selecting all the categories you want and set the profiles for each, scroll down to the bottom of the page and click the "Save the Configuration" button.