The problem with playing Clue cards with only 2 people is that the game is far too easy to solve and deduction and inference are rarely required.
With just one extra player the game takes on a completely different challenge. This is what CluePal brings to the table so to speak.
Start by taking out one card out of each type (weapon, place and suspect). Put those aside for the virtual player. Now deal out the rest of the cards to yourself, your fellow player and the virtual player.
Next, look at your cards and note the evidence that you have.
Start CluePal, pick out the evidence that you've been dealt and press Player One Deal.
Give the mobile device to your friend and have them do the same.
Now you're ready to play! Start playing the game as you normally would. Whenever you have to ask the virtual player, enter two items that you would like to inquire about and the virtual player should respond accordingly.
Once you think you have solved the mystery, press the solve button to see the crime and confirm that you've won.