The seek bar in a custom interface

I've been looking at the interface design options and I have a few questions. I used a seek bar in a recent experiment, where clicking buttons plays different audio. I had put the audio files in separate layers, and consequently the seek bar acted a little differently: audio clips that were shorter still worked against the same seek bar length of time, so that the shorter clips had long segments of blank audio at the end. Also the replay button was not operative. 

First, am I correct that the seek bar is not an available option for custom interface designs that don't use the built-in menu controls? Second, is there a preferred way to have multiple audio files on the same screen? I tried it with and without layers, so I'm wondering if I missed something. Or perhaps, is this question why so many of the eLearning examples available don't use the built-in controls at all?

Thanks!