You're confusing AE's effects environment with a video editor or program assembler. Audio is best mixed in an editor.
If you want to stay in AE, you must increase the length of the comp to accommodate your video clips, learn how to set and edit keyframes, and learn how to import and mix audio.
Here's what I'd do:
Output the Ae file and bring it back into Premiere for adding your music and editing transitions form slides to video and back to slides.
Use the template to get the video clips just barely started and then cut to the video full screen. run the video and then make a transition back to yoru slide show. do this again for your other video clip.
*woohoo* Here's to the ones daring marriage... For your problems there is a number of ways to tackle them, but the specific solution may depend on how the template works. As David already said, for audio you'd be better off using Premiere, but assuming you have just a single track that realyl only requires fades, AE should serve your needs. You can reveal the audio volume by tapping the L key when the respective layer in your composition is selected, then enable the stopwatch icon to add keyframes. Layers can be trimmed by simply dragging their ends, duplicated with Ctrl+D and split by using Ctrl+Shift+D, so it should be perfectly possible to extend your audio as needed, assuming you increase the comp duration first via the composition options. For the images to come into view, you could simply scale them up. Of course the project is based on 3D layers, so it would look a lot better if you animated the camera to dolly in, but if you have no experience in AE, that may make more of a mess than it's worth. Therefore I simply recommend you create a photo flash/ film burn transition - add a white solid with a slight color tint, set it's blending mode to add, animate it's opacity and while it's fading out, fade in your full screen video. If done in 32bpc, this can look quite real and since it's a separate effect, it won't interfere with the rest of the animation.
Thanks guys for your replies. Well it is certainly a start and will give me a nudge to start having a go. I think I should be able to keep it all contained within AE as the audio file (will drop in very last) will simply just fade whilst the videos play (videos only around 60 seconds each). I have heard much about the stop watch icon to add/edit keyframes but can I see this icon anyway? I must be missing something.
Regarding your suggestion re the camera dolly. that does sound cool. Again, if I knew how to use the keyframes I think I could do the camera dolly (if it is like flash in how it uses keyframes then I would like to try). If it is more of hard work to do that, then I will try your adding a transition and flash/burn etc. I think you got a bit too technical there though but would be good if you could expand a little more into a step by step? But the dolly zoom sounds great if I could pull that off.
Many thanks again - it's a great start and a bit of weight off the shoulders.