You can quickly configure message tracking logging through the Exchange Management Shell (EMS). Among the things you can set up are: the time the logs are to be kept, where they should be stored, the individual log file size, the total maximum size for the tracking logs directory, etc.

Retrieve the current settings for a server with:

Get-TransportServer <server-name> | Select MessageTracking*

Change those values with:

Set-TransportServer <server-name> <parameters>

In case your mailbox role is running on different servers, you also need to run:

Set-MailboxServer <server-name> <parameters>

Example: set the message tracking log for a server called EXCH01 to   ...