From the homepage, click Power Tools → Policy → Travel Policy.
The screen will default to Air policy, where you can adjust the following settings:

This sets rules for favored carriers, the scope of the preference (will it be "preferred" across the board, only when traveling to specific cities, etc), and the tolerance level of the preference (will all non-preferred carriers be out-of-policy, or are the preferred carriers just suggestions). For example:

Define how your preferred airlines should be sorted in the flight search results.
Choices include:
Note: Flights that are defined as unreasonable by your reasonable flights policy will always be sorted below reasonable flights regardless of the airline's preferred status.
(Click Travel Policies in the left-hand navigation list to return to the main Air page at any time.)
This selects air carriers that should be considered always out of policy.
This is set by traveler group. Click on [Traveler Group's name] to toggle the preferences for that group.
Some sample policies might be:

This determines whether flights must be booked within a specified minimum and maximum number of days from selected departure date. If a flight is booked too many or too few days prior to departure date, it will be marked as being out of policy. Keep in mind that all flight options will be marked as out-of-policy if a traveler performs an air search outside this window.
These definitions are set by Traveler Group. Click on the group you want to work with.

In this section you can specify limits for departure time windows, maximum trip duration, and maximum number of connections. From these specifications a Reasonable Flight definition is determined. Your Reasonable Flight settings determine the Lowest Logical Fare for any given search, but does not mark anything out-of-policy.
The Lowest Logical Fare is the lowest in-policy fare matching your Reasonable Flight settings.
For example, the overall least expensive flight from New York to Seattle for a VIP at your company may be priced at $311, with 1 connection. If your company allows a maximum of 0 connections for that VIP traveler group, then the Lowest Logical Fare for your itinerary would need to be a different flight (a direct flight or with no connection) at $361 - it is the lowest fare that meets your requirements.
This sets the tolerance level for the price of a flight as compared with the Lowest Logical Fare. Click on a Traveler Group to determine the tolerance range for that group. Here you can decide whether or not mark bookings that exceed your Lowest Logical Fare by a certain amount as being out of policy.
Choose a base airport and specify the alternate airports you want travelers to consider. ("When the user searches for ____, also search for these nearby airports ____ | ____ | ____.") This policy is enforceable by Traveler Group (with an option for reasonable flight consideration). Also specify comparison airports for reporting purposes: enter an airport you would like the booked fare to be compared against. Comparison information will appear in the new Alternative airports savings comparison report.
For example:

For travelers going to San Francisco (SFO), listings will also appear for flights going into Oakland (OAK) and San Jose (SJC). If a traveler chooses an OAK flight, your reports will show both the OAK ticket cost and compare it to the lowest logical fare the system records for an equivalent SFO flight.
This determines whether or not to allow your travelers/arrangers to purchase Web fares. Web fares are usually lower priced flights with strict change and cancellation policies, and are usually non-refundable - budget concern versus need for flexibility.
Your air policy is now set.