I don't believe themes and InstantMovies give you that much control, Dan. It's sort of the nature of it being so automatic. Sorry.
You can right-click on the finished InstantMovie on your timeline and select the option to break it apart, and then you can re-arrange the pieces. But that's about it, as far as I know.
I did the break apart option you mentioned. If you move the clip in the sceneline instead of timeline will all the effects applied by the theme move as well?
The effects are applied to the individual clips. So, when you move them, the effects move with the clips.
BTW, you do know that the InstantMovie is only one of four ways to create slideshows in Premiere Elements, right? If you want to have more control over the clips and the order they appear in, you may want to try one of the other slideshow creation tools.
Just really getting into the software. I will look them up but what are the other slideshow creation tools. Do they apply affects and transitions as well.
Any help or suggestions are greatly appreciated.
1) You can create a slideshow using the Elements Organizer's slideshow creator tool. This is probably the most intuitive way.
2) You can gather photos in Project panel, right-click on the batch and use the slideshow creator included in that panel.
3) Or, of course, you can manually add your slides to your timeline and apply custom or preset effects.
My books cover these methods, the advantages of each and other tricks for working with slideshows, if you're interested.
I don't know about 8, but in 9 you can clear the checkmark next to "Auto Edit" to prevent the Theme from trimming and sequencing your clips.