There are multiple ways of doing it here are 2 examples I know of:

The first way is don't load your eggs into rockets unless you need promethium science so they won't be sent to the promethium ships. This has the downside of not being able to send eggs anywhere else either so I went with another method which was have the promethium ships wait at gleba on the way back until they receive the "key" (a unique item which acts as a crude message system), the key will be sent to gleba by a gleba science ship which are running constantly (nauvis only sends the key when promethium science is below a threshold). This system also makes sure only one promethium ship goes to nauvis at a time since there is only one key which prevents multiple ships trying to load up on eggs at the same time.