Check out the paper of Kontsevich-Rosenberg Noncommutative spaces and Noncommutative Grassmannian and related constructions. You will get what you want. i.e. the definition of properness and separatedness of presheaves(as functors, taken as "space") and morphism between presheaves(natural transformations).
Notice that these definitions are general treatment for algebraic geometry in functorial point of view,nothing to do with noncommutative.
Definition for separated morphism and separated presheaves
Let X and Y be presheaves of sets on a category A(in particular, CRingsop). We call a morphism XrightarrowY separated if the canonical morphism
XrightarrowXtimesYX is closed immersion We say a presheaf X on A is separated if the diagonal morphism:
XrightarrowXtimesX is closed immersion
Definition for strict monomorphism and closed immersion
For a morphism f: YrightarrowX of a category A, denote by Lambdaf the class of all pairs of morphisms
u1,u2:XRightarrowV equalizing f, then f is called a strict monomorphism if any morphism g: ZrightarrowX such that LambdafsubseteqLambdag has a unique decomposition: g=fcdotg′
Now we have come to the definition of closed immersion: Let F,G be presheaves of sets on A. A morphism FrightarrowG a closed immersion if it is representable by a strict monomorphism.
Example
Let A be the category CAff/k of commutative affine schemes over Spec(k), then strict monomorphisms are exactly closed immersion(classcial sense)of affine schemes. Let X,Y be arbitrary schemes identified with the correspondence sheaves of sets on the category CAff/k. Then a morphism XrightarrowY is a closed immersion iff it is a closed immersion in classical sense(Hartshorne or EGA)
Definition for proper morphism just follows the classical definition: i.e. universal closed and separated. You can also find the definition of universal closed morphism in functorial flavor in the paper I mentioned.
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