1. You could lower your levels - either individual channels, aux channels strips or the main output channel strip you are bouncing through.
2. You could try applying some compression/limiting
3. Please provide some system details and describe in more detail what you are doing. Other than the assumption that, as you posted this in the Logic 8 area, you are using Logic 8 pro or express, we have absolutely no info to go on.
Just a thought, but do you mean clipping as in distorting the wave or as in chopping the first few seconds off? Sometimes if you have midi or audio data right at the beginning of a project, Logic chops it off when you bounce. To solve this problem you just have to shift everything forward a few bars.