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No, it not the best pratice, you you want to customize ClicShopping, it's better to have you own template.
The process is simple,
1 - inside default template direcotry, copy the files
2 - recreate the architecture of the directory and copy the files
ClicShopping, override the default files by the new files.
Default template can be use when there is an upgrade, that's why it's not a best pratice to change something inside the directory