1.
For the popup try setting the wmode
to opaque. This will allow the player to respect z-indexes.
Example taken from flowplayer site
flowplayer("player", {
src:"http://releases.flowplayer.org/swf/flowplayer-3.2.18.swf",
wmode: "opaque" // This allows the HTML to hide the flash content
}, {
clip: {
url: 'http://stream.flowplayer.org/flowplayer-700.flv'
}
});
For more detailed info see the flowplayer wmode demo
2.
To pause the video you should be able to do something like this in your showpop function.
$f("player").pause();
See player docs for more info on this.