First create templates for the two passes in Vegas under Render As. For example, if you're using 3ivx set it's Encoder mode to Dual Pass - First Pass and save the template as 3ivx First Pass. Then save a template for the second pass (setting the right Encoder mode of course).
With the templates created you are ready to continue. Open your project in Vegas and start Batchrender Pro. Click Add. Check Currently open project. Leave the Auto checkbox checked.
By default Batchrender Pro automatically appends the fileformat and template to the filename, this is important for 2-pass rendering since you don't want to overwrite the first file. If you have previously selected not to add these to the filename you can right click the textbox under Render As and select Add template to autofilename.
Set the fileformat to Video for Windows and the template to your newly created template, 3ivx First Pass.
Click OK and repeat the process for the second pass. If you want to render out a separate audio file just use the same procedure, don't forget the Currently open project checkbox.
When you have added all the renders you want you can save this batch.
To use this batch in the future, just open a project in Vegas first then run Batchrender Pro and load the batch.