Hi Christian,
As Xan pointed out - you set all the options for files/apps/registry and export this template. Some options are part of migration task and cannot be exported via Console. That does not mean you cannot get to them. Easiest way for you to get hold of all options used during Console migration is to execute your migration task, then open Explorer and go to c:\program files\symantec\ghost\outgoing folder. There at some point you'll see file of some random name with extension of xml. Copy this file somewhere and rename it to SCMMigrationOptions.xml.
You can then feed this options file to migration Wizard just like exported template. Migration engine is identical for Console and Wizard migration - it is just different shell that drives it.
Anyway, back to your question. Options are plain xml file so once you opened it in say notepad and go down to the bottom of it, you'll see section "extraoptions". In this section you can specify profile type, names, compression levels, debugging levels etc. Unfortunately we do not provide any manual describing what are the options but once you saw them it is very easy to figure out what and how to use them.
BTW, this method will not suffer from the bug Xan mentioned earlier of exporting template and not getting children applications included.
Good luck!