Best Practices for HTML5 Output

Hi all,

My company has decided to skip the Flash output entirely and use the HTML5 output for both web and tablets. 

I have been a web developer for about 15 years and know how to pick the story_html5.html file as the index file for the project.

We also want to modify the player.css file to further customizes the UI a bit.  Is there a way to create a permanent CSS file that will not get overwritten with each course we publish, since each project gets its own? Would it be better to have an "override" CSS that would contain just the changes we want?

Also would doing this screw up the output for the iOS player for iPad?

Perhaps someone has developed a script of some sort that would automate some of the manual work involved.

I'd be interested in hearing what other people may be doing in this regard to push the envelope a bit!