Calculation of Microstrip Width
Inner copper width is applicable only to multilayer boards (more than two layers). The outer copper thickness is applicable to the two outermost layers. If you have a trace running inside the board on an inner layer, you would need to use the inner-layer copper thickness for the calculation. If your microstrip is running on either the top or bottom layer, then use the outer layer thickness. The substrate is the FR-4, and is its own thickness (core).

Here is an example of a 4-layer PCB stackup:



The "Top Layer" and "Bottom Layer" are your outer copper layers, so they would have the "Outer Layer Thickness". The "Prepreg" layers in the above image are a fiberglass weave that separates the "Top Layer" or "Bottom Layer" copper from the "Internal Ground Plane" or "Internal Power Plane" copper. The "Internal Ground Plane" and "Internal Power Plane" layers are the inner copper layers, so they have the thickness specified for that. The "Core" is the rigid fiberglass FR-4 that gives the PCB its strength.

You have not yet mentioned whether your board is 2-layer or multi-layer (more than 2). If it is only 2-layer then your "substrate height" in the calculator would be the thickness of the core itself (specified by the manufacturer). If you have a multilayer board your "substrate height" would likely be the thickness of the prepreg layer between the "Top Layer" and the "Internal Ground Plane" layer.