I've been through the Bethesda tutorial a couple times now but I am unsure of the answer.
I have a mod (not mine) that I like a lot, however I want to modify it to fit my needs.
This is not to publish or take credit for, JUST FOR ME.
If all I am doing is changing some contents in the mod, i.e. a container. Do I need to
duplicate the entire interior (like the Vault 74 tutorial). and change what I want or just change it
within the original mod?

Just change within the mod ie. when loading in the GECK, make it active.

Don't pay attention to that, it's not at all necessary to copy an existing cell in order to make a new one. You can start from scratch if you go into the top menu and go to World/Cells. If you right click on the menu in there, you'll be given the option to create a brand new cell. I'm not sure why the tutorial tells people to just duplicate an existing cell, it's very misleading and a clumsy way of doing things.

What if all I want is my mod (don;t make an active file when loading) to 'override' the existing authors mod, in that it replaces a few containers with one's I've scripted. Would i still need to create an interior, clone his (doesn't sound like it) or just drop my containers overtop the originals (and delete the originals?) Then save my changes to my own .esp?

Yes, if you like his cell and just want to change a few containers and such, just make your changes in that cell and save as a new .esp. As long as your .esp is after the original in the load order, your changes will override his base cell. There's no need to create a new cell.

Thank you for the help but I must be doing something wrong.
I fire up GECK. Load the plugin mod (which loads FalloutNV.esm).
I navigate to the interior I want to add the cabinet to, drag the object in, arrange it nicely.
Click Save then give my changes it's own name.
Load FOMM, make sure my plugin is loaded after the original mod.
Fire up FO:NV and no cabinet.

Any ideas? did I miss a step?

You might want to go over to the FO:NV forum. I have heard there are a lot of issues with the CS for NV. They would know better over there.

If the original mod is an esp - just edit that and don't create a new esp.
If you load an esp in the Geck, then make changes, but save as a new esp, the Geck will throw away your changes.
If you made a copy of the original esp, made changes, then put it later in the load order than the original mod - that won't work either unless the original cell is a vanilla one.