Camera Alignment?
 

I've been trying some anaglyph 3D and am not sure on the correct way to set up the cameras?

Can you be more specific?

Sorry are you spost to angle the cameras in or keep them parallel?

Keep them parallel.

the best would be to keep an angle relative to distance of subject, but without a way to monitor this, it is prefferably to keep camera parallel, and avoid subject coming too close.
if you are ready to build a simple support, you could add a graduated system that allows to set the angle with distances written on a wheel.
the best would be to have a small lcd monitor with a simple video mixer that shows the two camera's pictures superposed. but just the mixed + lcd drives you around $800.

for the mixer , i found a box that just make this, and do not require camera to be synchronized
Video Signal or Image Mixer, Video Dissolver, Video Fader, Video Combiner, Video Overlapper, Combine, Mix, Dissolve or Fade two Video Signals

the biggest problem with angled camera is it creates keystoning, so it must be corrected in post.