Sheridan, if your tool allows you to just save the files and upload them later you might finder it easier to use a dedicated tool to upload them.
That way you can specify the exact directory that they should be uploaded to, usually using a file manager style graphical interface.
Something like
FileZilla would do the trick nicely. As it's a more widely used application we would be able to offer better support as well, to be honest though it's fairly point and click (if I can use it anybody can
).