I'm new to using the GECK but I've worked with the TES construction kit to a comfortable degree - the problem is after creating the .esp file to work in and making some basic changes (like adding some items in and around Megaton) to test the GECK I selected the data file when I opened Fallout3 and the changes aren't appearing in the game world when I looked around for them. Is there possibly some simple step I'm missing to make my modifications appear?

Is Fallout3.esm above your .esp in the load order? Also do any other mods override the changes you made in any way?

Yup that's the problem - it's not that my mod was above the fallout3.esm, it was the Anchorage expansion that was sitting above it - I shifted the fallout3.esm to the top and it worked. Thanks for your help.