To definitively help you, we'd have to see some code as the pseudo-code you posted above doesn't really make sense. It's not clear where your beginscene, clear calls, endscene and presents occur with respect to each other.

EDIT: I made an error in the code I posted above with respect to setting the rectangles for the viewport and presentation. Don't know if that messed you up. Apologies.

lastly, the framework presents the image

It sounds like you're presenting the backbuffer just once. That's a bit more complicated than the simple sequence I posted above, which is intended to be straight forward.

Repeating what I posted above:

1. Set the viewport to one-half of the backbuffer.

2. Clear, BeginScene, draw, Endscene

3. Present one-half of the backbuffer to one-half of the client area of the window.

Repeat for the other half of the backbuffer and client area.

There are some semantics to straighten out. The viewport doesn't get presented or "do" a scene. The viewport determines what portion of the backbuffer gets cleared by Clear(), and drawn to. After the drawing is done, the Present call displays the results. Present takes several parameters (take a look at the docs). The first parameter is a pointer to a RECT that determines what portion of the backbuffer will be copied to the window client area. The second parameter is a pointer to a RECT that determines TO what portion of the client area the backbuffer will be copied.

So you're saying you cannot render both scenes for both viewports and then draw them in one call of present?

No, I didn't say that. It may be possible, though I didn't do it that way when I tried it out. It seems simpler (to me) to have a single drawing routine, set parameters in preparation for drawing, call the routine, set different parameters and call the routine a second time.

You certainly can't have 2 viewports active at one time. Further, Present doesn't do any drawing. Present copies all or a portion of the backbuffer to all or a portion of the window client area (as described above.)