If you wish to keep some parts of source code untouchable, just enable text filtration option, add tags pairs to the list and HTML Protect Center will skip the code between these tags during encryption process.

For example, filters (<H1>, </H1>) or (<STRONG>, </STRONG>) allow you to keep unchanged some important strings of source code so that the page will still have the ability to be indexed by search engine spiders.

If page contains SSI (server side includes) tags, just add (<!--#, -->) tag pair to the filter list.

To manage filter list, use Add/Delete buttons

Add - creates new line in filter list, so that you can edit text of starting and ending tags;
Delete - removes selected filter from the list.