I am afraid you are misunderstanding the "reader extension". To start off there the reader extension is simply for being able to save the document/form in adobe reader. If you for example try to make a form and don't reader extend it, you wont be able to save the form AT ALL after entering information in it. In that case you will only be able to print it out. If you haven't ever encountered it before I would suggest you try open a "non-reader extended" file in adobe reader to experience what that looks like.
To your actual question, as far as my knowledge, there is not possible to make a "silent" save without pop-up without some external folder level script (e.g. nothing that can be done simply in the form). This is due to security concerns, as you wouldnt want a file "process" taking place without the form users noticicing. I think you can understand what I mean.
So as far as saving the document by a button click, the saveAs() function is one of your best bets I would guess. At least that is my knowledge about the topic.