FTP is a protocol standard that is used by everyone. I haven't found a design application or FTP tool that didn't work with Bravnet yet. You just have to be careful of the configuration.

When your using something like Filezilla, you connect to your FTP host, navigate to your web site folders, and then upload your files. When you use the FTP built into a design application, the host, user ID, and password are the same. But the design application needs to know in advance exactly where to put your files. This is because the folders leading to your web site folder, are not writable by you. If you don't specify it correctly, you will just get a bunch of "failed write" messages.

There is usually a configuration parameter named "remote directory", or "remote folder", or something like that. The "remote directory" is the same path to your web site, that you used when you navigated manually. For example, if I had a free Bravenet web site named "dumbstuff.bravehost.com", when I connected via FTP I would see the "web" folder. Navigating through that, I would see a folder named "dumbstuff.bravehost.com". I would have to navigate into that folder to upload my files, because the root (/) and "web" folders are not writable by me. So, if I were using a design application to upload my files, I would set the "remote folder" parameter to "/web/dumbstuff.bravehost.com".