In general you just need to have Flamerobin connect to Embedded Firebird through local protocol, my setup with Firebird 1.5.3 (Firebird 2.0 RC3 is giving me troubles!) is:
1. Pick fbembed.dll from Firebird-126.96.36.19970-0_embed_win32.zip
2. Copy it to C:\Program Files\FlameRobin (the Flamerobin installation folder, whatever it's named
3. Rename it to fbclient.dll
4. Register a new server in Flamerobin, without specifying the hostname and port (leave them blank)
5. Register a new database under that server, if you correctly left the hostname blank it will try to connect to something like "sysdba@c:\program files\employee.fdb"
5.1. Specify a password, because Flamerobin seems to want it, but remember that it will not be checked in the embedded version (privileges still exist!!)
6. You might need to copy more files from the embedded distribution to the flamerobin folder, like firebird.msg for messages, firebird.conf, ib_util.dll and the whole "intl" folder for connections with specific charsets!
Note that this allows me to keep also Firebird 2.0 RC3 installed, network connection to firebird 2 databases (new OnDiskStructure) will work, while it will fail if you try to connect as embedded (local protocol)