From Developerworks, Enabling SCA-MQ integration via MQ bindings:

The MQ Bindings feature in WebSphere Integration Developer V6.0.2, simplifies interoperability between SCA and MQ applications, and makes it easier
to read and write native MQ messages to and from SCA applications.

If you are new to WebSphere Integration Developer and need to connect to MQ, this is the article for you.

Tip: When they create the end-point configuration (Figure 20), they choose to “Specify Properties for configuring WebSphere MQ resources”. This will create the MQ connection factories, Queue definitions and other assorted runtime resources at EAR deployment time. Your administrator will only be able to modify them once the ear is installed to the system. Also when the EAR is uninstalled the resources will be removed. If your administrator has modified the JNDI’s in the meantime, the work will need to be redone.

If you are developing as part of a real project, you should always choose the latter: “Specify JNDI for pre-configured WebSphere MQ resources”. This will allow your WebSphere server administrator to define and modify the resources as needed throughout the production life cycle. They will survive EAR reinstalls and give you full control over your server.