Bought OSX server for FTPing

[Altemose]

Only slight annoyance at the moment is laptops that are both on site and off site need 2 different sync profiles which both try to run when I turn on the computer (I want it to auto sync on startup).

Why do you have two different sync profiles?

In terms of the sync settings, is there a downside to the bidirectional synchronise option for normal folders and not system files?

No. If you are looking for seamless sync then that is the correct option. If you want to do backups then it is dangerous as if a file gets corrupted, it will then be overwritten in the backup. You should use the backup option for backups.

A good tip is to use SmartScan. When used on both volumes, it will dramatically decrease the time it takes to sync.