As you say, two options are scripting or using the SQL server export/import wizard.
I've used both (for the same database as it happens)
A third option is to use Visual StudioTeam System 2008 Database Edition GDR.
In terms of a one time export and import then I'd recommend going with the wizard. This is very safe and also very straightforward. Particulary as you are new to SQL server, you want to take the approach that minimizes the risk.
The only downside to doing it this way is that it is perhaps a little less transparent than the other methods.
On the project where I merged databases I ended up using the scripting method but that was mainly because I had a project that was already using GDR to merge incremental database updates, so adding in a data merge script to that was a simple task - all changes needed to go through DBAs who unfortunately weren't very SQL literate (I know!) so keeping all the processes similar was a must.
I also took some of my learnings from scripting the data and applied them to setting up my reference data scripts, so the effort of scripting was not a one time cost.
Either way, the most important tip I can give is to back up the databases before doing any work on them.