You don't have to stop anything from the application side.

Here are a couple of notes when running Synchronise DB:

1. Stop Dbvisit schedules

2. Make sure there is sufficient space on temporary location (both Primary & Standby servers) where the RMAN back will be placed

https://dbvisit.atlassian.net/wiki/display/UGDS7/Synchronize+a+Standby+Database+using+the+CLI

3. Note that this incremental backup and "Synchronising" process can take time as RMAN will be doing a full scan of the database files.

If you have extremely large files this can take time, especially the backup. The restore process will be much faster.

In some cases the backup process (step 2 in the second image) can take the same time as a normal full RMAN backup, but remember only the required blocks (changes) are backed up and the restore process will be substantially faster.

https://dbvisit.atlassian.net/wiki/display/UGDS7/Synchronize+a+Standby+Database+using+the+GUI

4. Once Synchronise DB is completed, enable Dbvisit schedules to continue shipping and applying of logs.

Also refer to the below link for different scenarios of synchronisation:

http://blog.dbvisit.com/synchronize-your-standby-database-using-dbvisit-standby/