Is there a way to integrate pay per click into Flash or do you have to have an html site?
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Yes, Pay per click is fine (AKA paid search).
Perhaps not a good idea for seach engine optimisation.
The difference, if your unsure is:
Search engine optimisation (SEO) are the search results that take up the majority of the page.
Paid Search are the results that appear at the top and down the right hand side of the page.
You will have no problems with a flash site.
Michelle C is right. Pay-per-click works even if you have flash.
Search engines send out "spiders" to crawl the web looking to see if your web site says what your description says it does. It can’t read flash or graphics, only text.
So if you want to use SEO, minimize the flash.