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Is there a command or a trick to tell Mathematica to not automaticly evaluate some cells?

I use the NMinimize function to calculates some coordinates and then use that data with Manipulate. When I run NMinimize, Mathematica automaticly runs Manipulate.

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Manipulate is based on Dynamic, so if output of Manipulate is already created, then it will dynamically update every time when related variables have changes.

If you want to stop such behavior of Mathematica, you need to stop dynamic update temporary. And Start it again when it is needed. You can do it through GUI or by usual Mathematica command FinishDynamic[]

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If I follow your description correction you want to restrict TrackedSymbols to only those directly controlled by Manipulate. This means that when a non-tracked Symbol definition is modified the Manipulate will be "out of date" until you move a slider, etc.

fn = Sin;

Manipulate[Plot[fn[x (1 + a x)], {x, 0, 6}], {a, 0, 2}, TrackedSymbols :> {a}]

enter image description here

Now when you update fn nothing should change:

fn = Tan;

enter image description here

But then when you move the a slider:

enter image description here

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