To open multiple masters in GECK, set this line in GECKCustom.ini:
bAllowMultipleMasterLoads=1
It's default setting is, bAllowMultipleMasterLoads=0, which allows only one master to be used in addition to Fallout3.esm.
FO3Edit is also very useful in doing cleanup like removing altered cells and so on in the the base game, from your mod.
Just be sure to alter your mod in FO3Edit and not the master.