Is there a problem if i put in the sitemap only the links from the mainpage includin the index page and i miss the links from the secondary pages because they are to many. Is this thing affects how google index the pages?
It won't have any problem with Google as you will be the one to suffer. The purpose of a sitemap is to let the SE know that you have a large number of links on your site that otherwise would not be found by Google. So why would you want to missout on your inner pages?