The Tiler Utilization and Renderer Utilization percentages measure the duty cycle of the vertex and fragment processing hardware, respectively. On the MBX, Tiler Utilization typically scales with the amount of vertex data being sent to the GPU (in terms of both the number of vertices and the size of the attributes sent per-vertex), and Fragment Utilization generally increases with overdraw and texture sampling.
In your case, the best thing would be to reduce the size of each vertex you’re sending. For starters, I’d try binning your atoms and bonds by color, and sending each of these bins using a constant color instead of an array. I’d also suggest investigating if shorts are suitable for your positions and normals, given appropriate scaling. You might also have to bin by position in this case, if shorts scaled to provide sufficient precision aren’t covering the range you need. These sorts of techniques might require additional draw calls, but I suspect the improvement in vertex throughput will outweigh the extra per-draw call CPU overhead.
Note that it’s generally beneficial (on MBX and elsewhere) to ensure that each vertex attribute begins on a 32-bit boundary, which implies that you should pad your positions and normals out to 4 components if you switch them to shorts. The peculiarities of the MBX platform also make it such that you want to actually include the W component of the position in the call to glVertexPointer in this case.
You might also consider pursuing alternate lighting methods like DOT3 for your polygon data, particularly the spheres, but this requires special care to make sure that you aren’t making your rendering fragment-bound, or inadvertently sending more vertex data than before.