Will PHP included html content affect my seo?

Question

Today i purchase a small CMS system. With this CMS i can transform my static site into an editable page. I have to cut the content which i want to make editable, and paste it in

Answer 1

But if i delete my text and replace them with includes, how this will affect to SEO? (bots read my source, or read my source after php include my text-content?)

Not at all, PHP is server side, and thus it's outputed HTML will have the same SEO affect as your previous html files

May i instert the newly generated HTML files into my sitemap.xml?

Yes

May i exclude bots from my CMS directory (this directory contain the generated html files too) via htaccess?

Yes, in your robots txt file disallow them from accessing the folder. Also most likely your cms is password protected so the bots shouldn't have access