Each matter can have a standard or non standard default rate. In addition, each time entry can modified with a different rate.
As an example, rates are set under Setting->My Settings.
This is where you would set your primary rate and then set the alternative Travel rate.
In the Matter, you then set the preferred default rate.
The default rate will be applied to all time entries unless otherwise noted. To change a specific time entry, use the Advance button on the top of the time entry. When the advance option is applied, you can then override the default rate and apply a non-standard rate for that specific entry.