Universal Email uses the following command to over ride the servers script timeout settings:
by doing this, the script should be able to run for as long as is needed to send the emails. If your script is timing out anyway, it is because the host has prevented the timeout settings from being changed at the PHP level.
The email limits it's not so much that the script breaks the emails into batches, as the script waits the amount of time you specify between each email to send the next one. If it has reached the maximum number of emails and has not reached the Time limit for that max, it waits again till it can start sending the next email.