For the first option, you are asking to save the queued transfers so that they can be reloaded when Yummy FTP starts up again. This feature is on my To Do list, but I didn't get around to it yet. I will get to it

For the second option, currently this is a limitation of the Synchronize feature - only one connection is used. However, like the queued transfers, I have plans to allow it in a future update. This is much easier to add than saving the queue though, so it's likely to appear much sooner
