There are four important aspects of this:
1) You must have sufficient bandwidth from the computer where the SQLyog Job Agent (SJA) is running to the computer(s) hosting the servers. It is "half of the solution" to run SJA on one of the server machines, if it is possible. Remember SJA is available for Windows as well as for Linux.
2) The computer where SJA is executed must be powerful enough (and not too much burdened by other tasks) to perform the calculations needed to decide which operation should be performed on the servers. Remember: all these calculations are performed at the client running the SJA.
3) Server configuration(s). You might experience that bandwidth is not utilized and CPU-utilization at the client used for the job is very low too. That simply implies that the client is waiting for the server(s). You, your Sys Admin, or the support at the remote host(s)/ISP(s) should then review the server configuration(s). For heavy and intensive use of the Synchronization Tool it might be a good idea to pay somewhat additional for your database access. Most "personal" and "small-business" subscription plans are OK for an occasional sync. But in case you need to to sync huge amounts of data several times per hour you probably will need more resources at the remote network and database server.
4) You should learn to use the Synchronization tool effectively. There are several options available that reduces the amount of data transferred and the number and complexity of calculations that needs to be done. The most important aspects are:
- use a Primary Key for every table where it is possible.
- use the <columns> -option to only do calculations on a limited set of columns.
- use the <sql_where> - option to limit the number of rows that are tested for the need to sync.