OJS doesn't have an explicit SEO implementation, but it does for example include various tweaks to make it more searchable by Google and others (eg. http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=3838
). You can, if you want, modify the URLs that OJS provides by using a combination of Apache's mod_rewrite (much information via a forum search), and using OJS' Public Identifier capabilities (again, much info on the forum).
There's also a ton of information on creating and editing templates on the forum, as well as on Smarty.net
(that's the templating system we use). You will also probably want to take a look at the MVC architecture information in the OJS Technical Reference, available on the documentation page