How do I determine my Linux box's performance bottleneck?
Solution 1:
Check the utilization of the following things besides the processor,
- The 2GB RAM (if you are beyond 80%-90%, you need more of it)
- Swap space (If you find more than 30%-40% utilization, Disk I/O may slowing you down)
- Disk I/O (journaling and disk access speed may be holding you)
Checking Disk I/O is a good idea,
I'd also suggest checking the notes in EvilChookie's answer (+1 there),
particularly because you have an Atom based system.
An idle processor could also be a processor waiting for data/instructions.
Solution 2:
The SYSSTAT utilities consist of a great collection of performance monitoring tools for CPU, memory, Disk I/O, and your network.
The official tutorial can be found here.