In step 4 of the Magic Movie Wizard is a "Reorder" button that you can click and then rearrange the clips to your liking.
I believe if you use the timeline for the source, then the order the clips are in on the timeline is what is going to be the order in the movie.
Gateway DX4380, AMD A8-5500 Quad Core 3.2GHz with ATI Radeon HD 7560D; 16GB RAM; 1 TB SATA 7200 RPM; Windows 8 Pro 64-bit; PDR11, PDVD12.