You may practice and do the examination with either kind of transmission
The transmission you do your exam with, will decide wether or not your driver's licence will be limited to an automatic transmission
NOTE:
Legally, the person accompanying you on your examination ride may have a licence limited to automatics, even with a manual transmission car ..
However: GOCA and Flanders will disallow you to do your exam in that case
They incorrectly claim the accompanying person must be allowed to drive the exam car
(which may make sense, but is NOT the law ... which only requires an unspecified driver's licence B)