You should have three boxes - bank, sub-bank, and preset.
When you say the one at the top left always has the same patch in it, do you mean the bank one? That will have either the name of the bank (usually the person who wrote the patches) or else `all' - meaning it'll give access to all sub-banks regardless of who may have written the patches in them.
So it'll stay the same so long as you're in the sub-bank for that person's patches, or so long as you're in `all' mode.
So bank and sub-bank are like folder locations, and only the third window, the one called `preset' has indivdual files in it.
So are we talking about the same things?
It sounds like you've renamed the sub-bank when you say "That's not where I named my new preset but rather in the box that is to the right of the "Preset" box that has the down arrow on it."
The patch should never be overwritten when you've clicked `save as.' But if you've changed the name of the sub bank, that may make sense of what you've said.
I think you'll probably find you've created a duplicate sub bank if you've clicked save as. If that's the case the original patches will still be there and you'll have in effect another folder with the same patches, altered by your editing.
Hope that helps.