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Where do I need to put the code manually?

You can put the code in your template single.php and page.php. The most common place is after the post content just like similar/related post, or after the comment form.

Do I still need to edit my template if I choose to display the list automatically after blog content?

No, you don't need to. The list of search terms will automatically added after your blog content. The result will represent the display options you set in the 'Setting - SEO SearchTerms 2' admin menu.

I prefer comma separated keywords, how can I achieve that?

• Go to 'Admin > Settings > SEO SearchTerms 2' admin menu,
• Empty 'Text and code After and Before the list' column,
• Empty 'Text and code Before each keyword' column,
• And put ', ' (comma followed by space) in 'Text and code After each keyword' column.

I didn't see any change in my single post page, how do I know that the plugin working properly?

The plugin will not display the search term tags until there are any visitor coming from search engine into that blog post, until then, it's still invisible. So please wait until the plugin record any incoming visitor from search engine. Or you can search your own blog post from search engine to test it.