Sounds like you've identified the problem. 1.) If it's too high, then lower the pickup. Get out a small phillips head and turn the mounting screws for the pickup. Figure out which way makes it go down. But this probably isn't neccessary. 2.) Use your thumb against the last fret on the bass, not out above the pickup. 3.) Practice. It just flat takes a while to find out how your hand works during a slap/pop style. Mix and Match any of the above advice to taste.
<ol> <li>Don't move so far away from the body when you make your slaps, work on staying close to your strings and slapping with short thumb movements.</li> <li>Practice your aim.</li> </ol>
What tuning are you in? If you're palying in standard tuning than either your pickup's are way too high, or your bridge is way too low. You don't mean Fieldy slap do you? , if so it's your tuning. I hear heaps of guy's saying they play Korn songs on a down tuned 4 string, and tuning the E string down to A. Nothing sounds worse