The SBS that I'm sat in front of at the moment has three SQL Instances on it. Two came "out of the box" and one was done via the method that Darkwater describes above. If you look at the list of running services you'll probably see "MSSQL$SBSMONITORING" and "MSSQL$SHAREPOINT", and in my case also "MSSQLSERVER".
I'd stay clear of installing another non-default instance name as I've seen it cause issues with MDS Services (although this was a couple of service packs ago).
If you want a "manager" front-end for MSDE you could do worse than try here: English Home Page English - DbaMgr e DbaMgr2K
There's also the "osql" command line as well - RIM's pages tend to include osql examples and although it's not clicky pointy you can do most things that way if you have to.