Yes, the transaction timeout is editable within WSAD, but only by using the WebSphere Administration console. In WSAD, pick your WebSphere server and make sure the "Enable Administration console" box is checked. Then start your server. Then open a browser and type
http://localhost:9090/admin to open the admin console.
In the Admin console, pick the Servers tree and select your application server. In the Application Servers page for your server, pick the "Transaction Service" under "Additional Properties". On this page you can change the transaction timeout from the default (120 seconds) to a larger value. Make sure you press "Apply" and also that you Save your application server configuration.
You will then probably get a notice in WSAD indicating that your server has changed. Accept the changes.
Kyle