How do I go about being able to select multiple master files for when I'm making mods (I want to do a mod that will require a lot of resources from the DLC's but can't select all of them.) Would I be right in assuming it's an .ini file edit job?

Thanks!

Yes.
From the GECK FAQ:

How do I load multiple masters in the GECK?

To load multiple .esms in the GECK, you need to change this setting in the GECKCustom.ini file:
bAllowMultipleMasterLoads=1

Also from the category 'Data Files' on the GECK pages

To load multiple .esms in the GECK, you need to change this setting in the GECKCustom.ini file:

bAllowMultipleMasterLoads=1
This file is NOT found in the fallout3 folder in the BethesdaSoftworks folder. It is found in the user folders underMy Documents/My Games/Fallout 3

GECK page - http://geck.gamesas.com/index.php/Main_Page

I've navigated to the Fallout 3 folder in the My Games section but can't fine the GECKCustom.ini file. What now?

It resides in the same folder as all your fallout save games and the fallout.ini file.
If your sure you are looking in the right folders: My Documents/My Games/Fallout 3, then maybe you are still using all vanilla GECK settings and the GECK has had no reason to create a custom .ini file.

So, load up the GECK and change a setting under file/preferences, then the custom.ini file should be there.

-Mal

That worked! Thank you!!