If you have, say, 100 particle movieClips, use swapDepth to put the movieClip you want on top to be at a level 101 or more on load.
But there are many ways to create particles, if you can put them all in one master clip, you could easily put another clip on a higher layer on the stage (however, this would effect your paths).
I actually had a code creating 100 particles floating across the screen. By writing an actionscript onto the movie clip called "tv" on-stage, I was able to swap depths with the particle movie clip.