Firstly, be sure to upgrade to the latest version of Presence:-
It's always a good idea to have the latest version for the latest improvements (such as improved logging and load balancing) as well as making support simpler.
The changes.txt file located in the Presence directory will let you know what has changed between versions:-
In the Presence Bin directory on the machine where the database server is located you will find the sqltool.exe and databasecompactor.exe applications.
These can be used to manage and compact the database respectively.
To free up space in the database, run the sqltool.exe and perform a 'Truncate Table app.activityarchive' as well as a 'Truncate Table app.activityarchivehistory'
These tables store internal Presence information about who altered which task and when. The information is fairly verbose and over time uses up a lot of space.
Regular database compaction using the databasecompactor.exe tool.
Over time the database will expand as it is used. The database compactor enables you to straight forwardly, backup, unload and reload the database (thus compacting it).