The easiest way to render anaglyph in DirectX is to use the D3DRS_COLORWRITEENABLE renderstate, which controls which colour channels of the backbuffer you'll write to (the remaining channels are left unchanged).
So for red-cyan anaglyph, you might do something like this:
// only write to the backbuffer's red channel
// (draw left view here)
// only write to the backbuffer's green and blue channels
// (draw right view here)