Hey Rijwan,
We're making this easier in wyBuild 2.7 or 2.8, but you can still do it with wyBuild 2.6.x. There are a few ways you can do this.
For your main app you should should include the AutomaticUpdater in your main form, also add wyUpdate.exe and the client.wyc in your program's folder.
Now, for each of your modules you'll have a separate wyBuild project file. Also, you should store the modules in separate folders for the best results (least conflicts when updating). For instance, your folder setup should look something like this:
\YourApp\...wyUpdate.exe...client.wyc
...\Module1\...\Module1\YourFiles...\Module1\client.wyc
...\Module2\...\Module2\YourFiles...\Module2\client.wyc
Your main app will update the normal way (see the step-by-step walkthrough). Your modules you'll have to update a little differently. Instead of using the AutomaticUpdater to update your modules you'll have to use wyUpdate in standalone mode.
For instance, to silently check for update to "Module1" in the example, you would launch wyUpdate.exe something like this:
wyUpdate.exe -basedir="C:\Full Path\To\YourApp\Module1" -cdata="C:\Full Path\To\YourApp\Module1\client.wyc" -quickcheck
Of course you can use other commandline switches for silent checking (see: How to Silently Check for Updates) but the important ones are "-basedir" and "-cdata".
Tell me if this helps.