It would be really cool if we could have 2 windows. The behavior of the 1st window is just like the current version. Except you can select interesting nodes and copy them to the 2nd window where we can drag and pin them to positions within the window. This keeps their positions from jumping around while we try to understand the traffic among them.
Have you tried EtherApe -P option ? It allows you to position specific nodes in virtual columns. You need to know the fixed nodes in advance and it's not interactive, but it might still be enough.
From the manual: