On the Options tab there are a number of useful things you may wish to set.

The 'Sort before Send' option allows you to automatically sort your bookmarks before they are sent to the Server. There are a number of sort options available on the Advanced tab.
Normally, when you send your bookmarks and passwords, you will overwrite the bookmarks/passwords on your server. If the bookmarks on the server contained any changes you wanted to keep and hadn't yet received then these will be lost. The 'Send safely' option prevents this by always carrying out a receive first using the 'Only synchronise ...' and 'Merge ..' options described below. So the bookmarks on the server are received and merged into your local bookmarks/passwords first, and then sent to the server. So the whole process is a lot safer.
With the two 'Only synchronise ...' options SyncPlaces will checksum your bookmarks/passwords each time you send or receive them. It will then only send them again if this checksum doesn't match the current bookmarks/passwords. Each time your bookmarks/passwords are sent a small checksum (.sha1) file is also sent. When receiving, this file is obtained first and the bookmarks/passwords on the server only received if they have changed. So with this option you only send and receive bookmarks/passwords when needed saving time and bandwidth. Note that changing the server settings will throw away the checksums in case you are using a different path or server, so the next send/receive will always do something. Note: Older versions of SyncPlaces used checksum files with the extension '.ts' or '.hash' and these may now be safely deleted.
Normally the bookmarks in your local browser are replaced by the ones on the server when you click the 'Receive' button. Use the 'Merge bookmarks received' option to merge the server bookmarks with your local ones instead, so that you do not lose any new bookmarks or changes. Additional settings for this may be found on the Advanced tab.
Normally the 'Merge passwords received' option is turned on so that the passwords and password exceptions in your local browser are merged with the ones on the server when you click the 'Receive' button. Uncheck the 'Merge passwords received' option to overwrite the local passwords and exceptions with your server ones instead.
If you have a lot of bookmarks it may take a long time to transfer them. So you could use the 'Send/Receive compressed JSON' option, which will attempt to GZIP your bookmarks when sending them and GUNZIP them when receiving. So less data is transferred speeding up the whole process. My own bookmarks are transferred 6 times faster with this option, so it could make a big difference. NOTE: Remember that you must send your bookmarks in GZIP format first before receiving them or you will get a 'corrupt bookmarks' message. This option is not guaranteed to work for everyone, but it is safe to try.
The 'Encrypt JSON' option allows you to encrypt your bookmarks before sending and decrypt them on receiving using standard AES or the faster TEA encryption. You must also supply a password or 'key' for the encryption to work, and the longer this is the better. Note if you don't use the same password in two different browsers, or forget to turn this option on in one of them, then you will get a 'corrupt bookmarks' message. Because the extension does the encryption/decryption, the bookmarks will be stored in encrypted format on your server and so be unreadable. Note that encryption is a large overhead and so may significantly slow the transfer process.
You can automate the send/receive process using the options on this tab:

The 'Sync automatically' option will silently synchronise your bookmarks whenever they change. To cater for multiple changes in short succession the synchronisation happens when there have been no further changes for 5 seconds. The same logic also applies to the 'Sort automatically' option as well which will sort your bookmarks whenever they change. Setting the 'Sync automatically' option will automatically set the 'Send safely' option described above, so that each time it runs it will receive, merge and then send (but only if there's anything to do).
The 'Receive on startup' and 'Send on shutdown' options allow you to receive the latest bookmarks from the server when Firefox starts and sends them when you close Firefox.
The 'regular intervals' option allows you to automatically synchronise your bookmarks/passwords/exceptions at regular intervals, and is fairly self-explanatory. This option also needs a Firefox restart to begin working, but once running the interval can be dynamically changed or the automation stopped without having to restart again.
The 'set time' option allows you to Synchronise at a specific time - as long as Firefox is running at that time. Again, this option will automatically set and use the 'Send safely' option. Note that the actual time the synchronisation happens may be up to 5 minutes after the time you set.
Note: When any of the above options are used they operate completely silently, unless there is an error in which case a pop-up window will appear.