You'll need to write some javascript to change the src
of the iframe.
For a start, get your app working so that links will not open Safari by using something like the following (it's using jquery by the way):
if (window.navigator.standalone) {
$(document).on(
"click",
"a",
function (event) {
event.preventDefault();
var aurl = $(event.target).attr("href");
if (aurl) {
location.href = $(event.target).attr("href");
}
else {
location.href = this;
}
}
);
}
then you'll need to modify it to work with iframes too.
For more iphone app stuff you'll want to look at this: