SubscriptBox[x, y] represents in input and output.
Inside \( ... \) SubscriptBox[x, y] can be input as x \_ y.
In a notebook a SubscriptBox can be created using - or _. moves out of the subscript.
In StandardForm and InputForm, SubscriptBox[x, y] is interpreted on input as Subscript[x, y].
The baseline of SubscriptBox[x, y] is taken to be the baseline of x.
SubscriptBox[x, y] is usually output with y in a smaller font than x.
With the option setting LimitsPositioning->True y is placed in an underscript position when the whole SubscriptBox is displayed large, and in a subscript position when it is displayed smaller.
In StandardForm, explicit SubscriptBox objects are output literally. You can use DisplayForm to see the display form of such objects.
See The Mathematica Book: Section 2.8.10.
See also: SuperscriptBox, SubsuperscriptBox, UnderscriptBox, ScriptSizeMultipliers.