In HTML-based output formats the layout of topic pages in your output is defined in an HTML file called an HTML page template.
This template exists in your project but the project version is normally not used because you will almost always publish to these formats using a skin. Then the template used in the skin is used, and this will have been configured appropriately by the skin designer.
If you are designing a skin yourself you can find the template in the same location as described below, but in the .hmskin skin file instead of in your project. If you are editing one of the standard skins included with Help+Manual you always need to make a copy of it in your project folder to be able to edit it. You can then open it in Help+Manual by selecting .hmskin as the file type to open in the Open dialog. All the components in skins are in the same locations as in normal Help+Manual projects.
Kindle and ePUB use a special template generated by Help+Manual that is only stored in the project. It is available in Configuration > Publishing Options > eBooks > ePUB + Kindle: Page Template.