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 another location, keep them 6 months (180 days), and set the maximum limit to 4 GB:

Set-TransportServer EXCH01 -MessageTrackingLogMaxAge 180.00:00:00 -MessageTrackingLogMaxDirectorySize 4096MB -MessageTrackingLogPath T:\TrackingLogs

Note on setting MaxAge and MaxDirectorySize

The maximum directory size takes precedence over the maximum age, so be sure to set a size large enough to hold the number of days you specified for maximum age. If not sufficient, logs will be deleted anyway to be compliant with the maximum directory size. How much this has to be, depends entirely on the traffic volume. A good practice is to have it run for a week to get an idea of the log generation for a week, then adjust the maximum directory size accordingly to be able to maintain the maximum age of logs.