CmapTools contains a tool that can arrange your Cmaps in a logical manner.
From an open Cmap:
Select Format, then Autolayout...
If you want to do Autolayout on the entire Cmap, do not have any concepts or linking phrases selected.
On larger Cmaps, you can use Autolayout on parts of the Cmap by selecting the objects you wish to format.
This will open the Autolayout window.
The two tabs (Hierarchial & Force Directed) near the top of this window contain options for different ways of formatting the Cmap.
The Hiearchial options will layout the Cmap in a very structured, organized manner, often discarding the Cmap's existing design.
The Force Directed options will will reduce the amount of space between objects, keeping the Cmap's existing design.