It depends on how you send a SMS. There are 2 ways to create a new message. Method 2 will provide the solution to your problem.
Method 1 :
- Open the Contact profile either from People app or Call history
- If you have 2 numbers stored in the same profile/contact you will see only one text button below.

Clicking on this will send the Message to the first number in the mobile category.
Note : Text option is not shown for number stored in Home category even if it is the only number present.

Method 2 : This method is a solution to your problem too.
- Open Messaging app.
- Click on the plus sign located at the bottom.

- Now type the contact name at the top. As Rowland Shaw said it will Auto suggest contacts numbers. As you can see in the picture, both numbers of the contacts are shown.

Now you can select a number to send message to.