I am making my first mod every and the changes I make don't save.

My mod is an add-on to Morrowind Rebirth.

So I load the construction set up and load Morrowind, Bloodmoon, Tribunal.esm, Morrowind Rebirth.esp and my mod.

All the objects I place save, but when I delete a object from Morrowind Rebirth it always comes back when I load it up again.

My active File is my mod.

How do I fix this?

Basic question: do you make your mod active, by clicking "Set As Active File" with you plugin selected, prior to loading them?

yes.

All the objects I place save, but when I move or delete objects that are modified/placed by Morrowind Rebirth.esp they don't save.

I'll try to explain it better.

I delete a tree that is there from Morrowind Rebirth. I place a house where that tree was and save. I exit the construction set and reopen it.

The House I placed is still there, but the tree I deleted is also still there.

I can't seem to make changes to objects that Morrowind Rebirth places.

You could try:
if A.esp does not need to be loaded after some other .esp:
1. make A.esp a A.esm (with Mash/copy to .esm), and use A.esm as master for B.esp (faster to maintain with Mash updaters when A.esm changes)
, else
2. load A.esp and change it directly (may be hard to maintain when A.esp changes)

I did the first option and it worked.

I am new to modding so I find this odd as I want to release this, but won't it require everyone to have Morrowind Rebirth as an .esm?

Also the mod I am making adds a nice saw mill to Seyda Neen and the read me doesn't specify about usage.