The recently completed study of using one of the AFTA telescopes for a potential WFIRST mission included a coronagraph instrument for exoplanet imaging. The challenge is to design a coronagraph that achieves the desired high contrast in the presence of the complicated on-axis optical architecture of the AFTA. This is especially difficult if contrast levels as small as 10 -9 must be achieved at only 3λ/D from the star. In this paper we present shaped pupil designs using our new two-dimensional formulation. These designs also include constraints given by the wavefront control system, a necessary element of a complete high-contrast system in space. We have computed various shaped pupils for different contrast floors, inner working angles, and high-contrast region shapes. Two main types of masks are presented: discovery masks that offer wide discovery space with moderate inner working angles, and characterization masks which are designed for narrower discovery space and smaller inner working angles. Discovery and characterization masks would be used to image planets at different distances from the star at the same wavelengths, or to image the same planets at different wavelengths.