An Ipe drawing is a sequence of geometric objects. The order of the objects is important--wherever two objects overlap, the object which comes first in Ipe's sequence will hide the other ones. When new objects are created, they are added in front of all other objects. However, you can change the position of an object by putting it in front or in the back, using the functions in the struc menu.
Note, however, that due to the implementation of the LaTeX--Ipe interface, text objects in your drawing will always lie in front of everything else. It is not possible to cover a text object.
It is often convenient to treat a collection of objects as a single object. This can be achieved by grouping objects. The result is a geometric object, which can be moved, scaled, rotated etc. as a whole. To edit its parts or to move parts of it with respect to others, however, you have to un-group the object, which decomposes it into its component objects. Note that group objects can be elements of other groups, so you can create a hierarchy of objects.