Lowpass filters, EQ, and time stretch are your biggest friends. The more you single out the frequencies you want heard the more subtle and powerful they can become.
It is also important to remember to mix everything accordingly. Many people just layer and layer with out consideration of the conflict in frequencies. If you are adding a ton of low end with your sound design you may need to take away some low end from your music. If you want to have some sound design, a track and voice you need to take away a lot of frequencies and really focus on what you want each sound to be making. Having a muddy mix can make even great sound design sound dull and confusing. Remember there is only so much space in the mix it cant all be overlapping and conflicting with each other.