LHCb makes use of CMT (Configuration Managment Tool) to manage the physical organisation of packages and their interdependencies. All LHCb software (SICb, Gaudi/Brunel and also Outer Tracker Testbeam) is managed under CMT. For now at NIKHEF CMT is available only under Linux from bfys-accounts by running a configuration script. In case you use CMT also for Tracking group you have to run some additional scripts after running the general scripts. An introduction how to use LHCb software can be found on the CERN LHCb Software Twiki pages. A local wiki-page describes the implementation at Nikhef.
How to run Bender on stoomboot? See the Bender tutorial!
Alignment issues and trigger issues are delt with at the CERN LHCb pages.