Well the short and snarky answer is there are no options to allow Flash to show on iPads and iPhones. It doesn't support Flash at all.

The longer answer depends on what the Flash is and how important it is to the website experience. Anything key to the experience will have to be recreated in HTML and/or Javascript. A good way to do this is to detect whether your viewer has Flash and show them either the Flash movie or some fallback content. SWFObject is a good choice for this.

Another option would be to create a completely separate mobile version of the site. That may be a good option if the site is more Flash than HTML.