On my unit, presets and system are 5.6, modules are 5.61. These are not necessarily the same – we use the System version as the name, since it usually changes most often.
Once they are updated, you should indeed download the database with Vsig.
You should not need to update your user presets unless one of the modules they use was changed, in which case it will suggest you do so.
You should not need to change any sigfiles, unless there was a major change to one of the modules, such as a change to the number of ins or outs. We try and avoid such changes for this reason.