Lay down a modern map next to the biblical map. This will help you orient modern geographical boundaries and features with biblical geography. For example, find a map of the Mediterranean to compare with a biblical map illustrating the missionary journeys of Paul.
Follow the notes on the biblical map to understand what is trying to be depicted. In the example of Paul's journey, there usually three to four journeys reflected on the map, the first being from Antioch to Derbe. Read through all the journeys, which can include multiple trips. Paul's first journey, for example, reflects not just Antioch to Derbe, but Derbe to Antioch.
Locate the ancient locations on the map based on the places indicated. This can be tricky because the place names are largely different from modern place names. If you can't locate the place immediately, read through other locations indicated on the map until you see a familiar name. In the case of the biblical map of Paul's journeys, you'll see Jerusalem and Rome appear as locations. Locate both of these familiar locations on the map and work backwards from there.
Read the Bible entry in conjunction with the map. This will help you understand the time frame and story behind what is being shown on the map. It is also helpful to look at other details on the map, such as the scale, which will give you a better sense of the actual distances between places.