This is a big topic with a wide range of possible answers, but I'll try and hit the main points.
If you upload an HTML galley to OJS, it basically embeds it within the HTML page display. You can see this in effect by viewing the page source to http://pkp.sfu.ca/ojs/demo/present/inde ... e/view/4/7
. Note that OJS doesn't strip away any duplicated HTML header code (the stuff like <html>, <head> information, etc.), so that some elements that should be unique to the page are duplicated; nonetheless, it's currently recommended practice to ensure that this code is included in your HTML galley. (We recommend that any HTML galleys should be validated before being uploaded.)
PDFs are handled differently depending on which version of OJS you are using. In older versions of OJS, they were displayed in a frame alongside the Reading Tools (if the Reading Tools were enabled); in more recent versions of OJS, they are displayed within an HTML object tag -- basically, they are embedded within the page itself, with an option to blow up to fullscreen or to download to the viewer's computer.
If you are using a fairly recent version of OJS, your authors have the option of including references separately, in which case they will be displayed on the abstract page, and separately below the HTML/PDF galleys. (OJS 2.3.3 also included a Citation Markup Assistant, which may be of use; see this page
for links to further information. That page also has information on the new way of displaying PDFs.)
We eventually hope to facilitate galley creation from within OJS, but we aren't close to that yet. There is currently a plugin (called the XML Galleys plugin, that you can find from Journal Management -> System Plugins -> Generic Plugins) that can create HTML and PDF galleys from a single uploaded XML galley. It is our eventual goal to have an entire XML-publishing backend in OJS and our other applications, which will convert certain supplied document types (eg. Word/Open Office files) into XML and provide a workflow from that to publishable HTML galley, probably using elements of the XML Galleys plugin. But as I said, we're not too close to that yet.
If you have any further questions, please let us know!