If you want to add any custom css code to the extension, then add them to the file components/com_eshop/themes/default/css/custom.css so that they will not be lost when you update EShop in the future.
EShop is a standard Joomla MVC extension so it works based on standard Joomla rules. Joomla allows you to overwrite output of any components and modules from the template (Checkout more about this here: http://docs.joomla.org/How_to_override_the_output_from_the_Joomla!_core) so EShop also allows you to do that easily.
Example: To overwrite output of product details page, you need to copy file: components/com_eshop/themes/default/views/product/default.php to folder templates/your_template/html/com_eshop/product/default.php and modify this file from the template.
Once the file is putted in the template folder, it will be used instead of the file in the EShop component. So in the future, if you update EShop, the your modifications will be not lost.
You should use overwrite output from the template in the case you just have some minor changes on a few of pages.
EShop allows you to develop your own theme to display the different pages in EShop as the way that you want. Themes are located in a sub-folder in components/com_eshop/themes/ folder with the structure as following: As you are seeing, the default themes include a default.xml file and 3 main folders:
To create a new theme for your store, you just need to copy the folder default, then rename it to your theme name (example fashion), rename the default.xml file to fashion.xml file, then open fashion.xml file to edit it with correct values. Finally, zip whole the fashion folder as a zip package and go to EShop -> Plugins -> Themes to install the your fashion theme from there.
After installing fashion theme, you should go to EShop -> System -> Configuration -> Layout tab to choose Fashion theme as the theme for your store.
You should create your new theme in the case you want to change whole of layout/style of EShop output pages.