You can also do this more selectively by choosing to Add folders from the Folder tab rather than create new Folders using the wizard and excluding certain folders. To do this display the Folders tab (new as of 2006 I believe) and All Descendents, and then select the folders you wish to Add, and then right click and choose Add. This will make it easier in large nested folder trees to exclude folders that you don't want to add, though as a tip you should make sure to display your folders by Local Path, otherwise it will display them by Name which will be very confusing.
One thing you may want to keep your eyes open for in the future is the ability to reconcile your local workspace with the server and then choose your actions and commit everything in a single operation (change package). This is similar to the approach that you are using in the View Compare/Merge tool, but in this case you are comparing a View with your local Working folder instead. As a result of this you should be able to see both the folders and the files that need to be uploaded to the server, check that everything is okay, and then commit everything together.
You may want to check with StarTeam Support/R&D or your account rep to see if this capability is still on the road map but I believe this was a planned feature when I last discussed it with them.