Updated to use DM Basic Rules v0.3 on 2015-02-15
First, fill in the number of characters in your party and their level. If characters in your party are at different levels, add multiple rows and include each group of characters with the same level in their own row. Next, press CALCULATE to see the encounter XP thresholds for the party.
For example, if you have four first-level characters, type 4 in number, and 1 in level. If you have three seventh-level characters and one eighth-level, type 3 in number, 7 in level, add a second row, and add 1 in number and 8 in level.
Second, fill in the number of monsters and the amount of XP that each one gives in a similar manner. Finally, press CALCULATE to see details about the encounter, and to get a difficulty rating for the encounter given your party.
Alternatively, check the "Use Challenge Rating (CR)" box, fill in the number of monsters and the CR for each monster rather than its XP level.