It is much easier to place sound effects in to an existing music core, than to try to start the music after a sound effect. An exception to this which I find effective is if the sound effect is so crucial to setting up the feeling of the song that it helps students to get the right feeling for what to play. My caution here is to make sure that students come in on the down beat of the measure. Sound effects are not time based, meaning they don't have to conform to the beat or metronome, especially sounds like rainfall or crowd applause. Students tendency is to wait until their sound dissipates and then come in with the music, regardless of what beat the metronome is on.
Sound effects can make very effective transitions between sections of music as well.
Students may have a tendency to 'throw in everything but the kitchen sink', so the technique of referring back to the starting plan can again be helpful. I usually put introductions and endings in last as well. They are much easier to create once you know what the music is. Using an overhead with an LCD panel so the whole class stays involved can be helpful as well, though is not critical if you keep the pace moving and keep kids creatively involved in the process. This let's the kids feel that what their creating is like the real thing and they will be a lot more involved.