Closed Captioning with CaptionSync allows you to upload batches of files using AST-Link. This article shows how to name your files.
If you are using AST-Link to submit files, it can save you some time to pay attention to the filenames you use. While AST-Link doesn't require that the filename be devoid of spaces and characters like commas, it will replace all of them with underscores before they are processed. As a result, all the result files you get back will have underscores in them. Filenames without spaces and other characters like &%$' are known in the unix/linux/web world as “nicely named files”.
And while having media filenames different than the result files doesn't cause issues for any player, it becomes a bit of a hassle keeping the two of them together. Probably the easiest thing to do is a batch remove of spaces or replace with underscore.
On the Mac this is extremely easy to do with the “Make Names Web-Friendly 2.4” Automator action. Download this Automator action and install the “Make Web Friendly” action (and if rest of them which come with if you're interested). Then launch Automator, choose Create Service, drag the “Make Web Friendly” action in and save it. It will now appear in Finder any time you control or right click on a file or group of files.
For Windows, there are numerous free utilities to do the same thing. Spacetornado Renamer worked fine for us and seemed pretty easy to use: